diff --git a/README.md b/README.md index 78c4d01..29952d8 100644 --- a/README.md +++ b/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`. diff --git a/ct_scan/dataset_description.json b/ct_scan/dataset_description.json new file mode 100644 index 0000000..b5f7620 --- /dev/null +++ b/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/)" +} diff --git a/ct_scan/derivatives/labels/sub-spleen2/ct/sub-spleen2_ct_seg-manual.nii.gz b/ct_scan/derivatives/labels/sub-spleen2/ct/sub-spleen2_ct_seg-manual.nii.gz new file mode 100644 index 0000000..b667286 Binary files /dev/null and b/ct_scan/derivatives/labels/sub-spleen2/ct/sub-spleen2_ct_seg-manual.nii.gz differ diff --git a/ct_scan/df_ref.csv b/ct_scan/df_ref.csv new file mode 100644 index 0000000..b7a5c9a --- /dev/null +++ b/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,,,,,,,,,,,,,, diff --git a/ct_scan/participants.tsv b/ct_scan/participants.tsv new file mode 100644 index 0000000..8c2d780 --- /dev/null +++ b/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 + diff --git a/ct_scan/sub-spleen2/ct/sub-spleen2_ct.nii.gz b/ct_scan/sub-spleen2/ct/sub-spleen2_ct.nii.gz new file mode 100644 index 0000000..5b1fab3 Binary files /dev/null and b/ct_scan/sub-spleen2/ct/sub-spleen2_ct.nii.gz differ diff --git a/df_ref.csv b/df_ref.csv index c0dc445..caa99a7 100644 --- a/df_ref.csv +++ b/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,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/df_ref_multi.csv b/df_ref_multi.csv new file mode 100644 index 0000000..24270ac --- /dev/null +++ b/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 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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,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/microscopy_png/df_ref.csv b/microscopy_png/df_ref.csv index f7b81dc..914c026 100644 --- a/microscopy_png/df_ref.csv +++ b/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,,,,,,,,,,,,,,,,,,,,,,,, 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