Update SEM example dataset (#4)

* samples.tsv: Add sample_type column

* samples.json: Remove LongName fields, add sample_type description

* participants.tsv: Add species column

* participants.json: Remove LongName field, add species description

* Remove Species, Channel and BitDepth from JSON metadata

* Replace FovWidth and FovHeight with FieldOfView as a 2-number array in
JSON metadata

* Modify PixelSize as a 2-number array in JSON metadata

* dataset_description.json: Update Name and BIDSversion

* Add derivatives/labels/dataset_description.json file

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

README.md

@@ -1,4 +1,8 @@
-# data_example_microscopy_sem
+# data_axondeepseg_sem
+SEM dataset for AxonDeepSeg (https://axondeepseg.readthedocs.io/)
+
+10 rat spinal cord samples with axon and myelin manual segmentation labels.
+
 Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
 
-Microscopy BEP031 version 0.0.2 (2020-09-21T09:21:00)
+BIDS version 1.6.0 - Microscopy BEP031 version 0.0.4 (2021-07-13T15:14:00)

dataset_description.json

@@ -1,5 +1,5 @@
-{
-	"Name": "data_example_microscopy_sem",
-	"BIDSVersion":"1.4.0",
-	"License": "MIT"
-}
+{
+	"Name": "data_axondeepseg_sem",
+	"BIDSVersion":"1.6.0 - BEP031 v0.0.4",
+	"License": "MIT"
+}

derivatives/labels/dataset_description.json

@@ -0,0 +1,5 @@
+{
+	"Name": "data_axondeepseg_sem labels",
+	"BIDSVersion": "1.6.0 - BEP031 v0.0.4",
+	"PipelineDescription": {"Name": "Axon and myelin manual segmentation labels"}
+}

participants.json

@@ -1,6 +1,8 @@
-{
-    "participant_id": {
-        "LongName": "Participant ID",
-        "Description": "Unique participant ID"
-    }
-}
+{
+    "participant_id": {
+        "Description": "Unique participant ID"
+    },
+    "species": {
+        "Description": "Binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+    }
+}

participants.tsv

@@ -1,9 +1,9 @@
-participant_id
-sub-rat1
-sub-rat2
-sub-rat3
-sub-rat4
-sub-rat5
-sub-rat6
-sub-rat7
-sub-rat8
+participant_id	species
+sub-rat1	rattus norvegicus
+sub-rat2	rattus norvegicus
+sub-rat3	rattus norvegicus
+sub-rat4	rattus norvegicus
+sub-rat5	rattus norvegicus
+sub-rat6	rattus norvegicus
+sub-rat7	rattus norvegicus
+sub-rat8	rattus norvegicus

samples.json

@@ -1,10 +1,11 @@
-{
-    "sample_id": {
-        "LongName": "Sample ID",
-        "Description": "Unique sample ID"
-    },
-    "participant_id": {
-        "LongName": "Participant ID",
-        "Description": "Participant ID from whom tissue samples have been acquired"
-    }
-}
+{
+    "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)"
+    }
+}

samples.tsv

@@ -1,11 +1,11 @@
-sample_id	participant_id
-sample-data1	sub-rat1
-sample-data5	sub-rat2
-sample-data9	sub-rat3
-sample-data10	sub-rat3
-sample-data11	sub-rat3
-sample-data12	sub-rat4
-sample-data14	sub-rat5
-sample-data15	sub-rat6
-sample-Maxo03img60	sub-rat7
-sample-V915	sub-rat8
+sample_id	participant_id	sample_type
+sample-data1	sub-rat1	tissue
+sample-data5	sub-rat2	tissue
+sample-data9	sub-rat3	tissue
+sample-data10	sub-rat3	tissue
+sample-data11	sub-rat3	tissue
+sample-data12	sub-rat4	tissue
+sample-data14	sub-rat5	tissue
+sample-data15	sub-rat6	tissue
+sample-Maxo03img60	sub-rat7	tissue
+sample-V915	sub-rat8	tissue

sub-rat1/microscopy/sub-rat1_sample-data1_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.18,
-    "FovWidth": 230,
-    "FovHeight": 166,
-    "Species": "rat",
+    "PixelSize": [0.18, 0.18],
+    "FieldOfView": [230, 166],
     "BodyPart": "CSPINE",
     "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
 }

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

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.093,
-    "FovWidth": 119,
-    "FovHeight": 89,
-    "Species": "rat",
+    "PixelSize": [0.093, 0.093],
+    "FieldOfView": [119, 89],
     "BodyPart": "CSPINE",
     "SampleFixation": "4% paraformaldehyde, 0% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
 }

sub-rat3/microscopy/sub-rat3_sample-data10_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.1,
-    "FovWidth": 74,
-    "FovHeight": 76,
-    "Species": "rat",
+    "PixelSize": [0.1, 0.1],
+    "FieldOfView": [74, 76],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
 }

sub-rat3/microscopy/sub-rat3_sample-data11_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.1,
-    "FovWidth": 77,
-    "FovHeight": 84,
-    "Species": "rat",
+    "PixelSize": [0.1, 0.1],
+    "FieldOfView": [77, 84],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}

sub-rat3/microscopy/sub-rat3_sample-data9_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.1,
-    "FovWidth": 76,
-    "FovHeight": 76,
-    "Species": "rat",
+    "PixelSize": [0.1, 0.1],
+    "FieldOfView": [76, 76],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}

sub-rat4/microscopy/sub-rat4_sample-data12_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.1,
-    "FovWidth": 82,
-    "FovHeight": 77,
-    "Species": "rat",
+    "PixelSize": [0.1, 0.1],
+    "FieldOfView": [82, 77],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}

sub-rat5/microscopy/sub-rat5_sample-data14_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.13,
-    "FovWidth": 247,
-    "FovHeight": 234,
-    "Species": "rat",
+    "PixelSize": [0.13, 0.13],
+    "FieldOfView": [247, 234],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}

sub-rat6/microscopy/sub-rat6_sample-data15_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.13,
-    "FovWidth": 150,
-    "FovHeight": 97,
-    "Species": "rat",
+    "PixelSize": [0.13, 0.13],
+    "FieldOfView": [150, 97],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}

sub-rat7/microscopy/sub-rat7_sample-Maxo03img60_SEM.json

@@ -1,8 +1,5 @@
 {
-    "PixelSize": 0.07,
-    "FovWidth": 140,
-    "FovHeight": 140,
-    "Channels": 1,
-    "BitDepth": 8,
+    "PixelSize": [0.07, 0.07],
+    "FieldOfView": [140, 140],
     "Environment": "exvivo"
-}
+}

sub-rat8/microscopy/sub-rat8_sample-V915_SEM.json

@@ -1,11 +1,7 @@
 {
-    "PixelSize": 0.07,
-    "FovWidth": 108,
-    "FovHeight": 77,
-    "Species": "rat",
+    "PixelSize": [0.07, 0.07],
+    "FieldOfView": [108, 77],
     "BodyPart": "CSPINE",
     "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
-    "Channels": 1,
-    "BitDepth": 8,
     "Environment": "exvivo"
-}
+}