Merge pull request #286 from neuropoly/bep031

Examples for Microscopy BEP031

Recently merged validator PR for BEP031, it is working as expected with the two new examples.

README.md

@@ -12,8 +12,8 @@ files**. These datasets can be useful to:
 **ALL RAW DATA FILES IN THIS REPOSITORY ARE EMPTY!**
 
 However for some of the data, the headers containing the metadata are still
-intact. (For example the NIfTI headers for `.nii` files, or the BrainVision data
-headers for `.vhdr` files.)
+intact. (For example the NIfTI headers for `.nii` files, the BrainVision data
+headers for `.vhdr` files, or the OME-XML headers for `.ome.tif` files.)
 
 Headers are intact for the following datasets:
 
@@ -117,6 +117,7 @@ bids-examples (in alphabetical order).
 - [ASL datasets](#asl-datasets)
 - [qMRI datasets](#qmri-datasets)
 - [PET datasets](#PET-datasets)
+- [Microscopy datasets](#microscopy-datasets)
 - [Multimodal datasets](#multimodal-datasets)
 
 ### EEG datasets
@@ -204,6 +205,13 @@ bids-examples (in alphabetical order).
 | pet004 | @mnoergaard   | PET, blood      |                                          |
 | pet005 | @mnoergaard   | T1w, PET        |                                          |
 
+### Microscopy datasets
+
+| name      | maintained by | description                                                                                     |
+| ----------| ------------- | ----------------------------------------------------------------------------------------------- |
+| micr_SEM  | @jcohenadad   | Example SEM dataset in PNG format with 1 sample imaged over 2 sessions                          |
+| micr_SPIM | @jcohenadad   | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each |
+
 ### Multimodal datasets
 
 | name                   | maintained by     | description                                                                                                                          | mri                   | meg | eeg | ieeg | genetics | link to full data                                              |

micr_SEM/README

@@ -0,0 +1,3 @@
+1 mouse spinal cord sample imaged over 2 sessions.
+Example dataset with empty images containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
+

micr_SEM/dataset_description.json

@@ -0,0 +1,10 @@
+{
+	"Name": "micr_SEM",
+	"Authors": [
+		"Etienne Bergeron",
+		"Marie-Hélène Bourget",
+		"Julien Cohen-Adad"
+	],
+	"BIDSVersion":"1.7.0",
+	"License": "CC0"
+}

micr_SEM/participants.json

@@ -0,0 +1,21 @@
+{
+    "participant_id": {
+        "Description": "Unique participant ID"
+    },    
+    "sex": {
+        "Description": "sex of the participant",
+        "Levels": {
+            "M": "male",
+            "F": "female"
+        }
+    },
+    "species": {
+        "Description": "Binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+    },
+    "strain": {
+        "Description": "string value indicating the strain of the species"
+    },
+    "strain_rrid": {
+        "Description": "research resource identifier of the strain of the species from https://scicrunch.org/resources/Organisms/search"
+    }
+}

micr_SEM/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex	species	strain	strain_rrid
+sub-01	M	mus musculus	C57BL/6J	RRID:IMSR_JAX:000664

micr_SEM/samples.json

@@ -0,0 +1,11 @@
+{
+    "sample_id": {
+        "Description": "Sample ID"
+    },
+    "participant_id": {
+        "Description": "Participant ID from whom tissue samples have been acquired"
+    },
+    "sample_type": {
+        "Description": "Type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)"
+    }
+}

micr_SEM/samples.tsv

@@ -0,0 +1,2 @@
+sample_id	participant_id	sample_type
+sample-A	sub-01	tissue

micr_SEM/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SEM.json

@@ -0,0 +1,11 @@
+{       
+        "Manufacturer": "Hamamatsu",
+        "ManufacturersModelName": "C4742-95-12G04",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SliceThickness": 1,
+        "TissueDeformationScaling": 98,
+        "PixelSize": [0.18, 0.18],
+        "PixelSizeUnits": "um"
+}

micr_SEM/sub-01/ses-02/micr/sub-01_ses-02_sample-A_SEM.json

@@ -0,0 +1,11 @@
+{       
+        "Manufacturer": "Hamamatsu",
+        "ManufacturersModelName": "C4742-95-12G04",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SliceThickness": 1,
+        "TissueDeformationScaling": 98,
+        "PixelSize": [0.18, 0.18],
+        "PixelSizeUnits": "um"
+}

micr_SEM/sub-01/sub-01_sessions.json

@@ -0,0 +1,8 @@
+{
+    "session_id": {
+        "Description": "Session ID"
+    },
+    "acq_time": {
+        "Description": "Time when the sample have been acquired"
+    }
+}

micr_SEM/sub-01/sub-01_sessions.tsv

@@ -0,0 +1,3 @@
+session_id	acq_time
+ses-01	2015-11-04T14:10:00
+ses-02	2015-11-05T11:15:00

micr_SPIM/README

@@ -0,0 +1,10 @@
+2 rat spinal cord samples from the same subject with 4 chunks each.
+Example dataset with empty images containing single plane illumination microscopy (SPIM) data to illustrate BIDS convention.
+
+For demonstration purposes, JSON metadata includes fictional `ChunkTransformationMatrix` and `ChunkTransformationMatrixAxis` fields corresponding to the following transformation for both samples:
+
+- All chunks are scaled by a factor 2 in the Y axis,
+- chunk-01 is at the origin
+- chunk-02 is translated by 5 um along X,
+- chunk-03 is translated by 3 um along Z,
+- chunk-04 is translated by 5 um along X and by 3 um along Z

micr_SPIM/dataset_description.json

@@ -0,0 +1,10 @@
+{
+	"Name": "micr_SPIM",
+	"Authors": [
+		"Etienne Bergeron",
+		"Marie-Hélène Bourget",
+		"Julien Cohen-Adad"
+	],
+	"BIDSVersion":"1.7.0",
+	"License": "CC0"
+}

micr_SPIM/participants.json

@@ -0,0 +1,15 @@
+{
+    "participant_id": {
+        "Description": "Unique participant ID"
+    },    
+    "sex": {
+        "Description": "sex of the participant",
+        "Levels": {
+            "M": "male",
+            "F": "female"
+        }
+    },
+    "species": {
+        "Description": "Binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+    }
+}

micr_SPIM/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex	species
+sub-01	M	rattus norvegicus

micr_SPIM/samples.json

@@ -0,0 +1,11 @@
+{
+    "sample_id": {
+        "Description": "Sample ID"
+    },
+    "participant_id": {
+        "Description": "Participant ID from whom tissue samples have been acquired"
+    },
+    "sample_type": {
+        "Description": "Type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)"
+    }
+}

micr_SPIM/samples.tsv

@@ -0,0 +1,3 @@
+sample_id	participant_id	sample_type
+sample-A	sub-01	tissue
+sample-B	sub-01	tissue

micr_SPIM/sub-01/micr/sub-01_sample-A_stain-LFB_chunk-01_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 0],
+           [0, 2, 0, 0],
+           [0, 0, 1, 0],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-A_stain-LFB_chunk-02_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix": 
+          [[1, 0, 0, 5],
+           [0, 2, 0, 0], 
+           [0, 0, 1, 0],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-A_stain-LFB_chunk-03_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 0],
+           [0, 2, 0, 0],
+           [0, 0, 1, 3],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-A_stain-LFB_chunk-04_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 5],
+           [0, 2, 0, 0],
+           [0, 0, 1, 3],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-B_stain-LFB_chunk-01_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 0],
+           [0, 2, 0, 0],
+           [0, 0, 1, 0],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-B_stain-LFB_chunk-02_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix": 
+          [[1, 0, 0, 5],
+           [0, 2, 0, 0], 
+           [0, 0, 1, 0],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-B_stain-LFB_chunk-03_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 0],
+           [0, 2, 0, 0],
+           [0, 0, 1, 3],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}

micr_SPIM/sub-01/micr/sub-01_sample-B_stain-LFB_chunk-04_SPIM.json

@@ -0,0 +1,19 @@
+{
+        "Manufacturer": "Miltenyi Biotec",
+        "ManufacturersModelName": "UltraMicroscope II",
+        "BodyPart": "CSPINE",
+        "SampleEnvironment": "ex vivo",
+        "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+        "SampleStaining": "Luxol fast blue",
+        "PixelSize": [1, 1, 1],
+        "PixelSizeUnits": "um",
+        "Immersion": "Oil",
+        "NumericalAperture": 1.4,
+        "Magnification": 40,
+        "ChunkTransformationMatrix":
+          [[1, 0, 0, 5],
+           [0, 2, 0, 0],
+           [0, 0, 1, 3],
+           [0, 0, 0, 1]],
+        "ChunkTransformationMatrixAxis": ["X", "Y", "Z"]
+}