diff --git a/README.md b/README.md index c06d402..78c4d01 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,23 @@ Light-weighted data for testing/tutorial # Content -* sub-unf01: BIDS folder with multiple contrast (T2w, T2star and T1w). Original image and derivatives (see below) from [ivadomed spine generic example repo](https://github.com/ivadomed/data_example_spinegeneric/releases/tag/r20200907) were resampled to 1mm isotropic and converted to Float32 to reduce repo size. Subject was randomly selected among the available subjects. Images were oriented according to RPI convention and were cropped with the following bounding box: x=[50, 181], y=[60, 201], z=[10, 26]. + +## MRI anat +* sub-unf01: BIDS subject folder with multiple contrast (T2w, T2star and T1w). Original image and derivatives (see below) from [ivadomed spine generic example repo](https://github.com/ivadomed/data_example_spinegeneric/releases/tag/r20200907) were resampled to 1mm isotropic and converted to Float32 to reduce repo size. Subject was randomly selected among the available subjects. Images were oriented according to RPI convention and were cropped with the following bounding box: x=[50, 181], y=[60, 201], z=[10, 26]. * `derivatives/labels/sub-unf01`: derivatives folder with the following labels: * `_seg-manual`: spinal cord segmentations for all contrasts, * `_lesion-manual`: dummy labels which are supposed to represent lesion segmentation. WARNING: these are *not* actual lesion segmentations, but are only here for the purpose of testing the workflow of `ivadomed` codebase. * `_labels-disc-manual`: dummy label (single voxel), which is supposed to represent disc label. WARNING: this is *not* an actual label that represent the anatomy, but is only here for the purpose of testing the workflow of `ivadomed` codebase. * bounding\_box.json: dictionary to test a specific function from `ivadomed/scripts/bounding_box.py`. * dataset\_description.json: this file is needed to described the dataset. +* df\_ref.csv: Used to test a specific function from `ivadomed/loader/utils.py`. * participants.csv: table with subject name and potential metadata. * temporary\_results.csv: Used to test `ivadomed/scripts/compare_models.py`. + +## Microscopy +* `microscopy_png`: BIDS dataset folder containing microscopy data in PNG format (Microscopy BEP031 version 0.0.2) +* `microscopy_png/sub-rat2` and `microscopy_png/sub-rat3`: BIDS subjects folders with SEM contrast. Original images and derivatives (see below) from [ivadomed data_example_microscopy_sem repo](https://github.com/ivadomed/data_example_microscopy_sem/tree/r20201008) were adapted for testing purposes. +* `microscopy_png/derivatives/labels/`: derivatives folder with the following labels: + * `_seg-axon-manual`: axon segmentation + * `_seg-myelin-manual`: myelin segmentation +* `microscopy_png/df_ref.csv`: Used to test a specific function from `ivadomed/loader/utils.py`. diff --git a/derivatives/dataset_description.json b/derivatives/dataset_description.json new file mode 100644 index 0000000..0e3e94c --- /dev/null +++ b/derivatives/dataset_description.json @@ -0,0 +1,5 @@ +{ + "Name": "Example derivative dataset", + "BIDSVersion": "1.0.2", + "PipelineDescription": {"Name": "Example derivative pipeline"} +} \ No newline at end of file diff --git a/df_ref.csv b/df_ref.csv new file mode 100644 index 0000000..7152ba9 --- /dev/null +++ b/df_ref.csv @@ -0,0 +1,9 @@ +AcquisitionMatrixPE,AcquisitionNumber,AcquisitionTime,BaseResolution,BodyPartExamined,ConsistencyInfo,ConversionSoftware,ConversionSoftwareVersion,DeviceSerialNumber,DwellTime,EchoTime,EchoTrainLength,FlipAngle,ImageOrientationPatientDICOM,ImageType,InPlanePhaseEncodingDirectionDICOM,InstitutionAddress,InstitutionName,InstitutionalDepartmentName,InversionTime,MRAcquisitionType,MagneticFieldStrength,Manufacturer,ManufacturersModelName,Modality,ParallelReductionFactorInPlane,PartialFourier,PatientPosition,PercentPhaseFOV,PhaseEncodingSteps,PhaseOversampling,PhaseResolution,PixelBandwidth,ProcedureStepDescription,ProtocolName,PulseSequenceDetails,ReceiveCoilActiveElements,ReceiveCoilName,ReconMatrixPE,RepetitionTime,SAR,ScanOptions,ScanningSequence,SequenceName,SequenceVariant,SeriesDescription,SeriesNumber,ShimSetting,SliceThickness,SoftwareVersions,StationName,TxRefAmp,datatype,extension,subject,suffix,filename,age,data_id,date_of_birth,date_of_scan,first_name,institution_id,last_name,pathology,sex +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,anat,.nii.gz,test002,T2w,sub-test002_T2w.nii.gz,,,,,,,,,- +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sub-test002_T2w_seg-manual.nii.gz,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,anat,.nii.gz,test003,T2w,sub-test003_T2w.nii.gz,,,,,,,,,- +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sub-test003_T2w_seg-manual.nii.gz,,,,,,,,, +260,1,12:33:7.032500,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,,0.00372,,9,"[0, 1, 0, -0.00523601, 0, -0.999986]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",ROW,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,,1,3D,3,Siemens,Prisma_fit,MR,2,1,HFS,81.25,259,,1,150,spine_generic,T1w,%SiemensSeq%_tfl,"HC1-7;NC1,2",HeadNeck_64,320,2,0.0601922,IR,GR_IR,_tfl3d1_16,SK_SP_MP,T1w,2,"[620, -7194, -9127, 77, 28, -20, -10, -23]",1,syngo_MR_E11,MRC35049,266.247,anat,.nii.gz,unf01,T1w,sub-unf01_T1w.nii.gz,-,unknown,-,unknwon,unknown,unknown,unknown,unknwon,unknown +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sub-unf01_T1w_seg-manual.nii.gz,,,,,,,,, +320,1,12:39:2.805000,320,SPINE,N4_VE11C_LATEST_20160120,dcm2niix,v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0,167006,2.5e-06,0.12,76,120,"[0, 1, 4.897e-12, 0, 4.897e-12, -1]","['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'DIS2D']",COL,Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5,IUGM,Department,,3D,3,Siemens,Prisma_fit,MR,3,1,HFS,100,422,0.8,1,625,spine_generic,T2w,%SiemensSeq%_tse_vfl,"HC5-7;NC1,2;SP1",Spine_32,320,1.5,0.533389,PFP,SE,_spcR_100,SK_SP_OSP,T2w,3,"[620, -7194, -9127, 77, 28, -20, -10, -23]",0.8,syngo_MR_E11,MRC35049,283.131,anat,.nii.gz,unf01,T2w,sub-unf01_T2w.nii.gz,-,unknown,-,unknwon,unknown,unknown,unknown,unknwon,unknown +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,, diff --git a/microscopy_png/dataset_description.json b/microscopy_png/dataset_description.json new file mode 100644 index 0000000..a23fee1 --- /dev/null +++ b/microscopy_png/dataset_description.json @@ -0,0 +1,6 @@ +{ + "Name": "data_example_microscopy_sem", + "BIDSVersion":"1.4.0", + "Version": "https://github.com/ivadomed/data_example_microscopy_sem/archive/r20201008.zip", + "License": "MIT" +} \ No newline at end of file diff --git a/microscopy_png/derivatives/dataset_description.json b/microscopy_png/derivatives/dataset_description.json new file mode 100644 index 0000000..0e3e94c --- /dev/null +++ b/microscopy_png/derivatives/dataset_description.json @@ -0,0 +1,5 @@ +{ + "Name": "Example derivative dataset", + "BIDSVersion": "1.0.2", + "PipelineDescription": {"Name": "Example derivative pipeline"} +} \ No newline at end of file diff --git a/microscopy_png/derivatives/labels/sub-rat2/microscopy/sub-rat2_sample-data5_SEM_seg-axon-manual.png 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differ diff --git a/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM_seg-myelin-manual.png b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM_seg-myelin-manual.png new file mode 100644 index 0000000..b7f79fa Binary files /dev/null and b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM_seg-myelin-manual.png differ diff --git a/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-axon-manual.png b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-axon-manual.png new file mode 100644 index 0000000..e0f1617 Binary files /dev/null and b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-axon-manual.png differ diff --git a/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-myelin-manual.png b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-myelin-manual.png new file mode 100644 index 0000000..3df956d Binary files /dev/null and b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM_seg-myelin-manual.png differ diff --git a/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png new file mode 100644 index 0000000..e0f1617 Binary files /dev/null and b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png differ diff --git a/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-myelin-manual.png b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-myelin-manual.png new file mode 100644 index 0000000..3df956d Binary files /dev/null and b/microscopy_png/derivatives/labels/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM_seg-myelin-manual.png differ diff --git a/microscopy_png/df_ref.csv b/microscopy_png/df_ref.csv new file mode 100644 index 0000000..f7b81dc --- /dev/null +++ b/microscopy_png/df_ref.csv @@ -0,0 +1,16 @@ +BitDepth,BodyPart,Channels,Environment,FovHeight,FovWidth,PixelSize,SampleFixation,Species,datatype,extension,run,sample,session,subject,suffix,filename,testParticipant,test_samples,acq_time_x,test_sessions,acq_time,test_scans +8,CSPINE,1,exvivo,89,119,0.093,"4% paraformaldehyde, 0% glutaraldehyde",rat,microscopy,.png,,data5,,rat2,SEM,sub-rat2_sample-data5_SEM.png,test-rat-2,test-data5,,,, +,,,,,,,,,,,,,,,,sub-rat2_sample-data5_SEM_seg-axon-manual.png,,,,,, +,,,,,,,,,,,,,,,,sub-rat2_sample-data5_SEM_seg-myelin-manual.png,,,,,, +8,CSPINE,1,exvivo,76,76,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,,data9,01,rat3,SEM,sub-rat3_ses-01_sample-data9_SEM.png,test-rat-3,test-data9,2000-01-01T13:45:30,test-ses-01,, +,,,,,,,,,,,,,,,,sub-rat3_ses-01_sample-data9_SEM_seg-axon-manual.png,,,,,, +,,,,,,,,,,,,,,,,sub-rat3_ses-01_sample-data9_SEM_seg-myelin-manual.png,,,,,, +8,CSPINE,1,exvivo,76,74,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,,data10,02,rat3,SEM,sub-rat3_ses-02_sample-data10_SEM.png,test-rat-3,test-data10,2001-01-01T13:45:30,test-ses-02,, +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data10_SEM_seg-axon-manual.png,,,,,, +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data10_SEM_seg-myelin-manual.png,,,,,, +8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,1,data11,02,rat3,SEM,sub-rat3_ses-02_sample-data11_run-1_SEM.png,test-rat-3,test-data11,2001-01-01T13:45:30,test-ses-02,2001-01-01T13:45:30,test-run-1 +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data11_run-1_SEM_seg-axon-manual.png,,,,,, +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data11_run-1_SEM_seg-myelin-manual.png,,,,,, +8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,2,data11,02,rat3,SEM,sub-rat3_ses-02_sample-data11_run-2_SEM.png,test-rat-3,test-data11,2001-01-01T13:45:30,test-ses-02,2001-01-01T13:46:30,test-run-2 +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png,,,,,, +,,,,,,,,,,,,,,,,sub-rat3_ses-02_sample-data11_run-2_SEM_seg-myelin-manual.png,,,,,, diff --git a/microscopy_png/participants.tsv b/microscopy_png/participants.tsv new file mode 100644 index 0000000..c386a2e --- /dev/null +++ b/microscopy_png/participants.tsv @@ -0,0 +1,3 @@ +participant_id testParticipant +sub-rat2 test-rat-2 +sub-rat3 test-rat-3 \ No newline at end of file diff --git a/microscopy_png/samples.tsv b/microscopy_png/samples.tsv new file mode 100644 index 0000000..6076e7a --- /dev/null +++ b/microscopy_png/samples.tsv @@ -0,0 +1,5 @@ +sample_id participant_id test_samples +sample-data5 sub-rat2 test-data5 +sample-data9 sub-rat3 test-data9 +sample-data10 sub-rat3 test-data10 +sample-data11 sub-rat3 test-data11 \ No newline at end of file diff --git a/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.json b/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.json new file mode 100644 index 0000000..ec656ec --- /dev/null +++ b/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.json @@ -0,0 +1,11 @@ +{ + "PixelSize": 0.093, + "FovWidth": 119, + "FovHeight": 89, + "Species": "rat", + "BodyPart": "CSPINE", + "SampleFixation": "4% paraformaldehyde, 0% glutaraldehyde", + "Channels": 1, + "BitDepth": 8, + "Environment": "exvivo" +} diff --git a/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.png b/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.png new file mode 100644 index 0000000..8c46eeb Binary files /dev/null and b/microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.png differ diff --git a/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.json b/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.json new file mode 100644 index 0000000..669f2bc --- /dev/null +++ b/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.json @@ -0,0 +1,11 @@ +{ + "PixelSize": 0.1, + "FovWidth": 76, + "FovHeight": 76, + "Species": "rat", + "BodyPart": "CSPINE", + "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde", + "Channels": 1, + "BitDepth": 8, + "Environment": "exvivo" +} \ No newline at end of file diff --git a/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.png b/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.png new file mode 100644 index 0000000..478a507 Binary files /dev/null and b/microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.png differ diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.json b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.json new file mode 100644 index 0000000..6b297d7 --- /dev/null +++ b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.json @@ -0,0 +1,11 @@ +{ + "PixelSize": 0.1, + "FovWidth": 74, + "FovHeight": 76, + "Species": "rat", + "BodyPart": "CSPINE", + "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde", + "Channels": 1, + "BitDepth": 8, + "Environment": "exvivo" +} diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.png b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.png new file mode 100644 index 0000000..c35cecc Binary files /dev/null and b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.png differ diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.json b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.json new file mode 100644 index 0000000..73168d4 --- /dev/null +++ b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.json @@ -0,0 +1,11 @@ +{ + "PixelSize": 0.1, + "FovWidth": 77, + "FovHeight": 84, + "Species": "rat", + "BodyPart": "CSPINE", + "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde", + "Channels": 1, + "BitDepth": 8, + "Environment": "exvivo" +} \ No newline at end of file diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.png b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.png new file mode 100644 index 0000000..e4fea35 Binary files /dev/null and b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.png differ diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.json b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.json new file mode 100644 index 0000000..73168d4 --- /dev/null +++ b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.json @@ -0,0 +1,11 @@ +{ + "PixelSize": 0.1, + "FovWidth": 77, + "FovHeight": 84, + "Species": "rat", + "BodyPart": "CSPINE", + "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde", + "Channels": 1, + "BitDepth": 8, + "Environment": "exvivo" +} \ No newline at end of file diff --git a/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.png b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.png new file mode 100644 index 0000000..e4fea35 Binary files /dev/null and b/microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.png differ diff --git a/microscopy_png/sub-rat3/ses-02/sub-rat3_ses-02_scans.tsv b/microscopy_png/sub-rat3/ses-02/sub-rat3_ses-02_scans.tsv new file mode 100644 index 0000000..8a4f979 --- /dev/null +++ b/microscopy_png/sub-rat3/ses-02/sub-rat3_ses-02_scans.tsv @@ -0,0 +1,3 @@ +filename acq_time test_scans +microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.png 2001-01-01T13:45:30 test-run-1 +microscopy/sub-rat3_ses-02_sample-data11_run-2_SEM.png 2001-01-01T13:46:30 test-run-2 \ No newline at end of file diff --git a/microscopy_png/sub-rat3/sub-rat3_sessions.tsv b/microscopy_png/sub-rat3/sub-rat3_sessions.tsv new file mode 100644 index 0000000..0795a81 --- /dev/null +++ b/microscopy_png/sub-rat3/sub-rat3_sessions.tsv @@ -0,0 +1,3 @@ +session_id acq_time test_sessions +ses-01 2000-01-01T13:45:30 test-ses-01 +ses-02 2001-01-01T13:45:30 test-ses-02 \ No newline at end of file