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Merge pull request #115 from imagejan/patch-1
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Fix link to BDV HDF5 format description
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tischi authored Sep 25, 2024
2 parents 70e793d + 1213ace commit 69350ad
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2 changes: 1 addition & 1 deletion specs/mobie_spec.md
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Expand Up @@ -136,7 +136,7 @@ Two different types of sources are supported:
The data is stored in a chunked format for multi-dimensional data. Currently MoBIE supports the following data formats:
- `bdv.n5` and `bdv.n5.s3`: the data is stored in the [n5](https://github.com/saalfeldlab/n5) data format. The [bdv n5 format](https://github.com/bigdataviewer/bigdataviewer-core/blob/master/BDV%20N5%20format.md) is used to store additional metadata about timepoints, the multi-scale image pyramid and transformations. To support data stored on s3, we extend the xml by custom fields that describe the s3 storage. See an example
[here](https://github.com/mobie/plankton-fibsem-project/blob/master/data/emiliania/images/bdv-n5-s3/raw.xml#L27).
- `bdv.hdf5`: the data is stored in the [HDF5](https://www.hdfgroup.org/solutions/hdf5/) data format, using the [bdv hdf5 format](https://imagej.net/BigDataViewer.html#About_the_BigDataViewer_data_format) to represent image metadata. This format can only be read locally and **does not** support remote access from an object store.
- `bdv.hdf5`: the data is stored in the [HDF5](https://www.hdfgroup.org/solutions/hdf5/) data format, using the [bdv hdf5 format](https://imagej.net/plugins/bdv/#about-the-bigdataviewer-data-format) to represent image metadata. This format can only be read locally and **does not** support remote access from an object store.
- `ome.zarr` and `ome.zarr.s3`: the data is stored in the [ome zarr file format](https://ngff.openmicroscopy.org/latest/), which contains all relevant metadata about transformations and the multi-scale image pyramid in the zarr file directly.
- `openOrganelle.s3`: the data is stored in the [open organelle data format](https://openorganelle.janelia.org/), which is based on [n5](https://github.com/saalfeldlab/n5). Currently, this data format can only be streamed from s3 and cannnot be opened locally. We have added it to support data made available throuhg the Open Organelle data platform and the support is still experimental.

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