Add PNG microscopy data and files for testing dataframe

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`.

derivatives/dataset_description.json

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+{"Name": "Example derivative dataset", "BIDSVersion": "1.0.2", "PipelineDescription": {"Name": "Example derivative pipeline"}}

df_ref.csv

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+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,,,,,,,,,

microscopy_png/dataset_description.json

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+{
+    "Name": "data_example_microscopy_sem",
+    "BIDSVersion":"1.4.0",
+    "Version": "https://github.com/ivadomed/data_example_microscopy_sem/archive/r20201008.zip",
+    "License": "MIT"
+}

microscopy_png/derivatives/dataset_description.json

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+{"Name": "Example derivative dataset", "BIDSVersion": "1.0.2", "PipelineDescription": {"Name": "Example derivative pipeline"}}

microscopy_png/df_ref.csv

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+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,,,,,,

microscopy_png/participants.tsv

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+participant_id	testParticipant
+sub-rat2	test-rat-2
+sub-rat3	test-rat-3

microscopy_png/samples.tsv

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+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

microscopy_png/sub-rat2/microscopy/sub-rat2_sample-data5_SEM.json

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+{
+    "PixelSize": 0.093,
+    "FovWidth": 119,
+    "FovHeight": 89,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "4% paraformaldehyde, 0% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

microscopy_png/sub-rat3/ses-01/microscopy/sub-rat3_ses-01_sample-data9_SEM.json

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+{
+    "PixelSize": 0.1,
+    "FovWidth": 76,
+    "FovHeight": 76,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data10_SEM.json

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+{
+    "PixelSize": 0.1,
+    "FovWidth": 74,
+    "FovHeight": 76,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

microscopy_png/sub-rat3/ses-02/microscopy/sub-rat3_ses-02_sample-data11_run-1_SEM.json

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+{
+    "PixelSize": 0.1,
+    "FovWidth": 77,
+    "FovHeight": 84,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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"
+}

microscopy_png/sub-rat3/ses-02/sub-rat3_ses-02_scans.tsv

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+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

microscopy_png/sub-rat3/sub-rat3_sessions.tsv

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+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