Create SEM example dataset (#1)

* initial version

* rename rat8

* rename derivatives

* rename ses- to sample -

* change derivatives

* add more details in json

* add more details json

* add more derivatives

* Update README.md

* Update README.md

* add extra files

* Update README.md

* update BodyPart

* fix typo

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

Co-authored-by: Julien Cohen-Adad <[email protected]>

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

Co-authored-by: Julien Cohen-Adad <[email protected]>

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

Co-authored-by: Julien Cohen-Adad <[email protected]>

* fix formatting

Co-authored-by: mariehbourget <[email protected]>
Co-authored-by: Julien Cohen-Adad <[email protected]>

.gitignore

@@ -0,0 +1 @@
+.DS_Store

README.md

@@ -1,2 +1,4 @@
-# data_microscopy_SEM_example
+# data_example_microscopy_sem
 Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
+
+Microscopy BEP031 version 0.0.2 (2020-09-21T09:21:00)

dataset_description.json

@@ -0,0 +1,5 @@
+{
+	"Name": "data_example_microscopy_sem",
+	"BIDSVersion":"1.4.0",
+	"License": "MIT"
+}

participants.json

@@ -0,0 +1,6 @@
+{
+    "participant_id": {
+        "LongName": "Participant ID",
+        "Description": "Unique participant ID"
+    }
+}

participants.tsv

@@ -0,0 +1,9 @@
+participant_id
+sub-rat1
+sub-rat2
+sub-rat3
+sub-rat4
+sub-rat5
+sub-rat6
+sub-rat7
+sub-rat8

samples.json

@@ -0,0 +1,10 @@
+{
+    "sample_id": {
+        "LongName": "Sample ID",
+        "Description": "Unique sample ID"
+    },
+    "participant_id": {
+        "LongName": "Participant ID",
+        "Description": "Participant ID from whom tissue samples have been acquired"
+    }
+}

samples.tsv

@@ -0,0 +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

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.18,
+    "FovWidth": 230,
+    "FovHeight": 166,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

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

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.1,
+    "FovWidth": 74,
+    "FovHeight": 76,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

sub-rat3/microscopy/sub-rat3_sample-data11_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"
+}

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.1,
+    "FovWidth": 76,
+    "FovHeight": 76,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.1,
+    "FovWidth": 82,
+    "FovHeight": 77,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.13,
+    "FovWidth": 247,
+    "FovHeight": 234,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.13,
+    "FovWidth": 150,
+    "FovHeight": 97,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

@@ -0,0 +1,8 @@
+{
+    "PixelSize": 0.07,
+    "FovWidth": 140,
+    "FovHeight": 140,
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}

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

@@ -0,0 +1,11 @@
+{
+    "PixelSize": 0.07,
+    "FovWidth": 108,
+    "FovHeight": 77,
+    "Species": "rat",
+    "BodyPart": "CSPINE",
+    "SampleFixation": "3% paraformaldehyde, 3% glutaraldehyde",
+    "Channels": 1,
+    "BitDepth": 8,
+    "Environment": "exvivo"
+}