New loader integration: update datasets (#13)

* Update df_ref.csv for MRI anat

* Update df_ref.csv for microscopy png

* Add df_ref.csv for multiple folders test

* Add ct_scan dataset folder

* Update README.md

* Update README.md

* Remove dataset_description.jon from ct_scan/derivatives folder

README.md

@@ -22,3 +22,10 @@ Light-weighted data for testing/tutorial
   * `_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`.
+
+## CT-scan
+* `ct_scan`: BIDS subject folder organized according to the file naming and structure of CT-scan BEP024 version 0.0.0 as of 2021-03-22. Original image (`Task09_Spleen.tar/imagesTr/spleen2.nii.gz`) and derivative (`Task09_Spleen.tar/labelsTr/spleen2.nii.gz`) from Simpson, A. L., Antonelli, M., Bakas, S., Bilello, M., Farahani, K., Van Ginneken, B., ... & Cardoso, M. J. (2019). A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv preprint arXiv:1902.09063, used under [CC-BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) license. Data available at [Medical Segmentation Decathlon](http://medicaldecathlon.com/). Images were cropped with the following bounding box: x=[(66, 230], y=[114, 280], z=[64, 98].
+* `ct_scan/sub-spleen2` : BIDS subject folder with CT-scan contrast (ct).
+* `ct_scan/sub-spleen2/derivatives/labels/`: derivatives folder with the following label:
+  * `_seg-manual`: spleen segmentation
+* `ct_scan/df_ref.csv`: Used to test a specific function from `ivadomed/loader/utils.py`.

ct_scan/dataset_description.json

@@ -0,0 +1,9 @@
+{
+  "BIDSVersion": "1.5.0",
+  "Name": "Spleen",
+  "Description": "Spleen Segmentation",
+  "Reference": "Memorial Sloan Kettering Cancer Center",
+  "Version":"1.0 06/08/2018, available at http://medicaldecathlon.com/, spleen2 image and label cropped from original",
+  "Study": "Simpson, A. L., Antonelli, M., Bakas, S., Bilello, M., Farahani, K., Van Ginneken, B., ... & Cardoso, M. J. (2019). A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv preprint arXiv:1902.09063",
+  "Licence":"CC-BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/)"
+}

ct_scan/df_ref.csv

@@ -0,0 +1,3 @@
+filename,datatype,extension,subject,suffix,participant_id,age,data_id,date_of_birth,date_of_scan,first_name,institution_id,last_name,pathology,sex
+sub-spleen2_ct.nii.gz,ct,.nii.gz,spleen2,ct,sub-spleen2,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown
+sub-spleen2_ct_seg-manual.nii.gz,,,,,,,,,,,,,,

ct_scan/participants.tsv

@@ -0,0 +1,3 @@
+participant_id	sex	age	first_name	last_name	date_of_birth	date_of_scan	pathology	data_id	institution_id
+sub-spleen2	unknown	-	unknown	unknown	-	unknown	unknown	unknown	unknown
+

df_ref.csv

@@ -1,5 +1,7 @@
-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
-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,-,unknown,unknown,unknown,unknown,unknown,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,-,unknown,unknown,unknown,unknown,unknown,unknown
-,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,,
+filename,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,participant_id,age,data_id,date_of_birth,date_of_scan,first_name,institution_id,last_name,pathology,sex
+sub-unf01_T1w.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,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown
+sub-unf01_T1w_lesion-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-unf01_T1w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-unf01_T2w.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,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown
+sub-unf01_T2w_lesion-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

df_ref_multi.csv

@@ -0,0 +1,15 @@
+filename,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,participant_id,age,data_id,date_of_birth,date_of_scan,first_name,institution_id,last_name,pathology,sex,acq_time,test_scans,BitDepth,BodyPart,Channels,Environment,FovHeight,FovWidth,PixelSize,SampleFixation,Species,run,sample,session,testParticipant,sample_id,test_samples,acq_time_x,test_sessions
+sub-rat2_sample-data5_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,microscopy,.png,rat2,SEM,sub-rat2,,,,,,,,,,,,8,CSPINE,1,exvivo,89,119,0.093,"4% paraformaldehyde, 0% glutaraldehyde",rat,,data5,,test-rat-2,sample-data5,test-data5,,
+sub-rat2_sample-data5_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-01_sample-data9_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,microscopy,.png,rat3,SEM,sub-rat3,,,,,,,,,,,,8,CSPINE,1,exvivo,76,76,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,,data9,01,test-rat-3,sample-data9,test-data9,2000-01-01T13:45:30,test-ses-01
+sub-rat3_ses-01_sample-data9_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-02_sample-data10_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,microscopy,.png,rat3,SEM,sub-rat3,,,,,,,,,,,,8,CSPINE,1,exvivo,76,74,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,,data10,02,test-rat-3,sample-data10,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-data11_run-1_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,microscopy,.png,rat3,SEM,sub-rat3,,,,,,,,,,2001-01-01T13:45:30,test-run-1,8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,1,data11,02,test-rat-3,sample-data11,test-data11,2001-01-01T13:45:30,test-ses-02
+sub-rat3_ses-02_sample-data11_run-1_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-02_sample-data11_run-2_SEM.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,microscopy,.png,rat3,SEM,sub-rat3,,,,,,,,,,2001-01-01T13:46:30,test-run-2,8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,2,data11,02,test-rat-3,sample-data11,test-data11,2001-01-01T13:45:30,test-ses-02
+sub-rat3_ses-02_sample-data11_run-2_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-unf01_T1w.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,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown,,,,,,,,,,,,,,,,,,,
+sub-unf01_T1w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+sub-unf01_T2w.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,-,unknown,-,unknown,unknown,unknown,unknown,unknown,unknown,,,,,,,,,,,,,,,,,,,
+sub-unf01_T2w_seg-manual.nii.gz,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

microscopy_png/df_ref.csv

@@ -1,16 +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,,,,,,
+filename,BitDepth,BodyPart,Channels,Environment,FovHeight,FovWidth,PixelSize,SampleFixation,Species,datatype,extension,run,sample,session,subject,suffix,participant_id,testParticipant,sample_id,test_samples,acq_time_x,test_sessions,acq_time,test_scans
+sub-rat2_sample-data5_SEM.png,8,CSPINE,1,exvivo,89,119,0.093,"4% paraformaldehyde, 0% glutaraldehyde",rat,microscopy,.png,,data5,,rat2,SEM,sub-rat2,test-rat-2,sample-data5,test-data5,,,,
+sub-rat2_sample-data5_SEM_seg-axon-manual.png,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat2_sample-data5_SEM_seg-myelin-manual.png,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-01_sample-data9_SEM.png,8,CSPINE,1,exvivo,76,76,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,,data9,01,rat3,SEM,sub-rat3,test-rat-3,sample-data9,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,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-02_sample-data10_SEM.png,8,CSPINE,1,exvivo,76,74,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,,data10,02,rat3,SEM,sub-rat3,test-rat-3,sample-data10,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,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-02_sample-data11_run-1_SEM.png,8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,1,data11,02,rat3,SEM,sub-rat3,test-rat-3,sample-data11,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,,,,,,,,,,,,,,,,,,,,,,,,
+sub-rat3_ses-02_sample-data11_run-2_SEM.png,8,CSPINE,1,exvivo,84,77,0.1,"3% paraformaldehyde, 3% glutaraldehyde",rat,microscopy,.png,2,data11,02,rat3,SEM,sub-rat3,test-rat-3,sample-data11,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,,,,,,,,,,,,,,,,,,,,,,,,