test_bfopen fails with #29

sbesson · 2019-07-23T13:50:10Z

While trying to create a minimal example file to reproduce https://forum.image.sc/t/bio-formats-octave-error-on-bfsave/27504, I realized that the current Travis build is failing - see https://travis-ci.org/ome/bio-formats-octave-docker/builds/545619855.

Populating metadata
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1

There are two issues associated with this error:

I would have expected the docker run command to fail with a non-zero status code on a failing script rather than a false negative
octave_base_value::reshape (): wrong type argument 'octave_java' is thrown when calling bfGetPlane for all recent builds using GNU Octave 4.2 / Bio-Formats 6. The only related report I could find was https://savannah.gnu.org/bugs/?44881. @carandraug: do you have any immediate thoughts on this before we start investigating.

The text was updated successfully, but these errors were encountered:

carandraug · 2019-07-23T16:07:06Z

I would have expected the docker run command to fail with a non-zero status code on a failing script rather than a false negative

I've checked on Octave 4.0 and Octave 6.0 and in both cases returns a non zero return code

$ touch "test&sizeT=3.fake"
$ octave travis_test.m "test&sizeT=3.fake"
[...]
s = 1
v = 6.2.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1
$ echo $?
1

octave_base_value::reshape (): wrong type argument 'octave_java' is thrown when calling bfGetPlane for all recent builds using GNU Octave 4.2 / Bio-Formats 6. The only related report I could find was https://savannah.gnu.org/bugs/?44881.

That issue is unrelated (the issue is about making reshape also work in java arrays and that is something that doesn't even work in Matlab). This error seems to be related to auto boxing/unboxing rules. In Matlab, it looks like I in:

I = javaMethod('makeDataArray2D', 'loci.common.DataTools', plane, ...
    bpp, fp, little, ip.Results.height);

returns a Matlab array of class int8 but in Octave this remains an octave_java object of class byte[][] which is why the switch statement fails. I believe that in Octave, arrays with more than one dimension remain a java object in case they are non-rectangular. This probably needs to be changed in Octave for sake of Matlab compatibility but I don't think there's anyone working in Octave at the moment that quite understands the different conversion rules that would be Matlab compatible.

sbesson · 2019-07-23T21:37:18Z

@carandraug: thanks for the quick reponse. The base image used for testing Octave is Ubuntu 18.04 which ships GNU Octave 4.2.2

octave@89da10fab560:~$ touch "test&sizeT=3.fake" 
octave@89da10fab560:~$ octave -version
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
GNU Octave, version 4.2.2
Copyright (C) 2018 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html to learn how to submit bug reports.
octave@89da10fab560:~$ octave travis_test.m "test&sizeT=3.fake" && echo passed
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
s = 1
v = 6.1.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test at line 9 column 1
passed
octave@89da10fab560:~$ echo $?
0
octave@89da10fab560:~$ exit

Switching to Ubuntu 16.04 and GNU Octave 4.0.0, I can confirm the status code is returned as non-zero as expected

octave@50c2a3c49946:~$ touch "test&sizeT=3.fake" 
octave@50c2a3c49946:~$ octave --version
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
GNU Octave, version 4.0.0
Copyright (C) 2015 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html to learn how to submit bug reports.
octave@50c2a3c49946:~$ octave travis_test.m "test&sizeT=3.fake"
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
s =  1
v = 6.1.0
FakeReader initializing test&sizeT=3.fake
Reading series #1
    .error: octave_base_value::reshape (): wrong type argument 'octave_java'
error: called from
    bfGetPlane at line 99 column 7
    bfopen at line 150 column 13
    test_bfopen at line 6 column 6
    travis_test.m at line 9 column 1
octave@50c2a3c49946:~$ echo $?
1

This seems related to http://octave.1599824.n4.nabble.com/Octave-s-exit-status-td4680966.html. It looks like the regression was fixed in 6.0 but did not make it into a patch release of Octave 4.2.x.

Thanks also for pointing at the autoboxing behavior. While bisecting changes introduced, I think this is effectively a regression introduced as part of ome/bioformats#3301.

jburel · 2023-12-13T11:07:31Z

The same problem occurs when testing on docker image Ubuntu 22.04 and octave 6.4.0

carandraug · 2023-12-13T12:37:50Z

I've looked at this and it works fine in bioformats 5.9.2 and started to fail in bioformats 6.0.0. @sbesson suggested and I confirm that the issue is a regression introduced in ome/bioformats#3301

It boils down to the description I had above:

This error seems to be related to auto boxing/unboxing rules. In Matlab, it looks like I in:
I = javaMethod('makeDataArray2D', 'loci.common.DataTools', plane, ...
    bpp, fp, little, ip.Results.height);
returns a Matlab array of class int8 but in Octave this remains an octave_java object of class byte[][] which is why the switch statement fails. I believe that in Octave, arrays with more than one dimension remain a java object in case they are non-rectangular. This probably needs to be changed in Octave for sake of Matlab compatibility but I don't think there's anyone working in Octave at the moment that quite understands the different conversion rules that would be Matlab compatible.

I will prepare a pull request.

…o-formats-octave-docker#29) Octave does not autobox multi-dimensional arrays (Matlab does) so we can't use makeDataArray2D. Instead, use makeDataArray to get a 1D array and reshape it. This commit partially reverts 3aa468e (see ome#3301) for Octave only, so the data copy is back but for Octave only.

carandraug · 2023-12-13T13:26:14Z

I will prepare a pull request.

Done in ome/bioformats#4130

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Updating 996da68..d566f70 Previously merged: - PR 4129 melissalinkert 'Bump version to 7.2.0-SNAPSHOT' - PR 4128 melissalinkert 'Update version numbers to 7.1.0' - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling' - PR 4126 dgault 'Bump dependency versions' Generated by BIOFORMATS-push#1662 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1662/)

Repository: ome/bio-formats-build Excluded PRs: - PR 552 dependabot[bot] 'Bump bioformats from `996da68` to `d566f70`' (user: dependabot[bot]) - PR 551 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `a291695`' (user: dependabot[bot]) - PR 550 dependabot[bot] 'Bump ZarrReader from `1d18bbc` to `4deea8d`' (user: dependabot[bot]) - PR 549 dependabot[bot] 'Bump bio-formats-examples from `6218db5` to `083f617`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Updating 1d18bbc..4deea8d Previously merged: - PR 70 dgault 'Bump version to 0.4.1-SNAPSHOT' Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Updating 6218db5..083f617 Previously merged: - PR 121 sbesson 'Bump version to 7.2.0-SNAPSHOT' - PR 120 sbesson 'Bio-Formats 7.1.0' - PR 119 sbesson 'Update OME artifactory repository to deploy to ome.releases' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Updating 996da68..d566f70 Previously merged: - PR 4129 melissalinkert 'Bump version to 7.2.0-SNAPSHOT' - PR 4128 melissalinkert 'Update version numbers to 7.1.0' - PR 4057 melissalinkert 'Add CodecOptions.disableChromaSubsampling' - PR 4126 dgault 'Bump dependency versions' Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1662 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1662/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Generated by BIOFORMATS-push#713 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/713/)

Repository: ome/bio-formats-build Already up-to-date. Merged PRs: - PR 469 jburel 'install sphinx' - PR 549 dependabot[bot] 'Bump bio-formats-examples from `6218db5` to `083f617`' - PR 550 dependabot[bot] 'Bump ZarrReader from `1d18bbc` to `4deea8d`' - PR 552 dependabot[bot] 'Bump bioformats from `996da68` to `d566f70`' - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' Repository: ome/ZarrReader Excluded PRs: - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Already up-to-date. Merged PRs: - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' Repository: ome/bio-formats-documentation Already up-to-date. Merged PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' Repository: ome/bio-formats-examples Already up-to-date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft) Already up-to-date. Conflicting PRs (not included): - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#713 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/713/)

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Generated by BIOFORMATS-push#1663 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1663/)

Repository: ome/bio-formats-build Excluded PRs: - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' (user: dgault) - PR 73 dgault 'Update ReadMe and Change Log' (user: dgault) - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Already up-to-date. Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1663 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1663/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Generated by BIOFORMATS-push#714 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/714/)

Repository: ome/bio-formats-build Already up-to-date. Merged PRs: - PR 469 jburel 'install sphinx' - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' Repository: ome/ZarrReader Excluded PRs: - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Already up-to-date. Merged PRs: - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' - PR 73 dgault 'Update ReadMe and Change Log' - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' Repository: ome/bio-formats-documentation Already up-to-date. Merged PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' Repository: ome/bio-formats-examples Already up-to-date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft) Already up-to-date. Conflicting PRs (not included): - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#714 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/714/)

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Generated by BIOFORMATS-push#1664 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1664/)

Repository: ome/bio-formats-build Excluded PRs: - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' (user: dgault) - PR 73 dgault 'Update ReadMe and Change Log' (user: dgault) - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Already up-to-date. Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1664 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1664/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Generated by BIOFORMATS-push#715 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/715/)

Repository: ome/bio-formats-build Already up-to-date. Merged PRs: - PR 469 jburel 'install sphinx' - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' Repository: ome/ZarrReader Excluded PRs: - PR 73 dgault 'Update ReadMe and Change Log' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Already up-to-date. Merged PRs: - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' Repository: ome/bio-formats-documentation Already up-to-date. Merged PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' Repository: ome/bio-formats-examples Already up-to-date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft) Already up-to-date. Conflicting PRs (not included): - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#715 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/715/)

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Generated by BIOFORMATS-push#1665 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1665/)

Repository: ome/bio-formats-build Excluded PRs: - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' (user: dgault) - PR 73 dgault 'Update ReadMe and Change Log' (user: dgault) - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Already up-to-date. Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1665 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1665/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Generated by BIOFORMATS-push#716 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/716/)

Repository: ome/bio-formats-build Already up-to-date. Merged PRs: - PR 469 jburel 'install sphinx' - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' Repository: ome/ZarrReader Excluded PRs: - PR 73 dgault 'Update ReadMe and Change Log' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Already up-to-date. Merged PRs: - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' Repository: ome/bio-formats-documentation Already up-to-date. Merged PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' Repository: ome/bio-formats-examples Already up-to-date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (label: exclude) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up-to-date. Merged PRs: - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' - PR 4112 melissalinkert 'Imaris HDF: populate channel names' - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft) Already up-to-date. Conflicting PRs (not included): - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#716 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/716/)

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Generated by BIOFORMATS-push#1666 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1666/)

Repository: ome/bio-formats-build Excluded PRs: - PR 553 dependabot[bot] 'Bump bio-formats-documentation from `f4a4045` to `45b07e2`' (user: dependabot[bot]) - PR 469 jburel 'install sphinx' (user: jburel) Already up-to-date. Repository: ome/ZarrReader Excluded PRs: - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions' (user: dgault) - PR 73 dgault 'Update ReadMe and Change Log' (user: dgault) - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0' (user: sbesson) - PR 20 dgault 'ZarrReader: Use chunk API' (user: dgault) Already up-to-date. Repository: ome/bio-formats-documentation Excluded PRs: - PR 355 dgault 'Adding checkerframework.org to link check ignore' (user: dgault) Updating f4a4045..45b07e2 Previously merged: - PR 356 melissalinkert 'Change ome-codecs version from 1.1.0 to 1.0.1' - PR 354 melissalinkert 'Update to 7.2.0-SNAPSHOT' - PR 353 melissalinkert 'Bump versions to 7.1.0' - PR 350 dgault 'Add link to Bioformats.NET6' - PR 352 dgault 'Add version history for Bio-Formats 7.1.0' - PR 349 dgault '7.1.0 API updates' - PR 343 dgault 'Add bio3d to link check ignore' - PR 351 dgault 'Bump dependencies to latest versions' Repository: ome/bio-formats-examples Excluded PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' (user: dgault) Already up-to-date. Repository: openmicroscopy/bioformats Excluded PRs: - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (user: dgault) - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' (user: carandraug) - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1' (user: ed-scanlon) - PR 4114 melissalinkert 'Add test for image names when resolutions are not flattened' (user: melissalinkert) - PR 4112 melissalinkert 'Imaris HDF: populate channel names' (user: melissalinkert) - PR 4111 melissalinkert 'OIR: channel order and missing pixel block fixes' (user: melissalinkert) - PR 4100 nicolapapp 'bug fix, thumb nails are unsigned integers, and exceeded 2^31, so I changed their size to Long' (user: nicolapapp) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4061 CGDogan 'Don't fail on non-4:4:4 JPEG' (user: CGDogan) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (user: melissalinkert) - PR 3872 arvequina 'New codec integration Jetraw' (user: arvequina) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (user: dgault) - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (user: dgault) Already up-to-date. Repository: ome/ome-codecs Excluded PRs: - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (user: dgault) Already up-to-date. Repository: ome/ome-common-java Excluded PRs: - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (user: dependabot[bot]) - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru) Already up-to-date. Repository: ome/ome-jai Already up-to-date. Repository: ome/ome-mdbtools Already up-to-date. Repository: ome/ome-metakit Already up-to-date. Repository: ome/ome-model Excluded PRs: - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (user: joshmoore) - PR 174 jburel 'Remove docs' (user: jburel) Already up-to-date. Repository: ome/ome-poi Already up-to-date. Repository: ome/ome-stubs Already up-to-date. Generated by BIOFORMATS-push#1666 (https://latest-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1666/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Generated by BIOFORMATS-push#267 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/267/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 659 dependabot[bot] 'Bump bioformats from `df36e69` to `ee508a0`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#267 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/267/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Generated by BIOFORMATS-push#268 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/268/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 659 dependabot[bot] 'Bump bioformats from `df36e69` to `ee508a0`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#268 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/268/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating ee508a0..862723a Previously merged: - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' Generated by BIOFORMATS-push#269 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/269/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 659 dependabot[bot] 'Bump bioformats from `df36e69` to `ee508a0`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating ee508a0697..862723aa15 Previously merged: - PR 4252 melissalinkert 'Leica TCS: make sure XML file is on used files list' Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#269 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/269/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' Generated by BIOFORMATS-push#270 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/270/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' (user: marcobitplane) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#270 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/270/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#271 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/271/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#271 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/271/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#272 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/272/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#272 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/272/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#273 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/273/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#273 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/273/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#274 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/274/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Merged PRs: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#274 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/274/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#275 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/275/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 658 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `8dc4ea1`' - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Merged PRs: - PR 394 pwalczysko 'Add sas.upenn.edu to ignore list linkchecker' Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Updating be5b189c..5d681a64 Previously merged: - PR 174 jburel 'Remove docs' - PR 192 jburel 'Remove py38' Merged PRs: - PR 193 jburel 'Build' Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#275 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/275/)

…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Generated by BIOFORMATS-push#276 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/276/)

Repository: ome/bio-formats-build Excluded PRs: - PR 632 dependabot[bot] 'Bump ZarrReader from `9a9e662` to `b17c3ab`' (status: failure) Already up to date. Merged PRs: - PR 660 dependabot[bot] 'Bump bioformats from `df36e69` to `862723a`' - PR 661 dependabot[bot] 'Bump bio-formats-documentation from `b07c8df` to `e2ec252`' - PR 662 dependabot[bot] 'Bump ome-model from `be5b189` to `908c6ef`' Repository: ome/ZarrReader Excluded PRs: - PR 95 dgault 'Class cast exception when parsing metadata' (status: failure) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) Updating 9a9e662..b17c3ab Previously merged: - PR 93 dgault 'Bump version to 0.5.3-SNAPSHOT' - PR 92 dgault 'Bump version to 0.5.2' - PR 91 dgault 'Bump Bio-Formats version to 7.3.1' Merged PRs: - PR 97 melissalinkert 'Bump Bio-Formats version to 8.0.1' - PR 98 dominikl 'Fix class cast and labels issue.' Repository: ome/bio-formats-documentation Already up to date. Repository: ome/bio-formats-examples Already up to date. Merged PRs: - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 4196 melissalinkert 'DICOM: use FrameTimePointer to detect timelapse data' (label: exclude) - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru) - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Already up to date. Merged PRs: - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' - PR 4195 WalkerKnapp 'Andor SIF: Support files larger than 4 GB and with non-fixed-size footers' - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4249 marcobitplane 'Imaris Reader: support for LZ4 compression and performance improvements' Repository: ome/ome-codecs Already up to date. Merged PRs: - PR 41 rharkes 'Add LZ4 compression/decompression' Repository: ome/ome-common-java Already up to date. Repository: ome/ome-jai Already up to date. Repository: ome/ome-mdbtools Already up to date. Repository: ome/ome-metakit Already up to date. Repository: ome/ome-model Already up to date. Repository: ome/ome-poi Already up to date. Repository: ome/ome-stubs Already up to date. Generated by BIOFORMATS-push#276 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/276/)

jburel mentioned this issue Dec 13, 2023

Clean up #55

Merged

carandraug linked a pull request Dec 13, 2023 that will close this issue

matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29) ome/bioformats#4130

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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…d use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29))

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test_bfopen fails with #29

test_bfopen fails with #29

sbesson commented Jul 23, 2019

carandraug commented Jul 23, 2019

sbesson commented Jul 23, 2019 •

edited

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jburel commented Dec 13, 2023

carandraug commented Dec 13, 2023

carandraug commented Dec 13, 2023

test_bfopen fails with #29

test_bfopen fails with #29

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sbesson commented Jul 23, 2019

carandraug commented Jul 23, 2019

sbesson commented Jul 23, 2019 • edited Loading

jburel commented Dec 13, 2023

carandraug commented Dec 13, 2023

carandraug commented Dec 13, 2023

sbesson commented Jul 23, 2019 •

edited

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