[ENH] BEP031: Microscopy

README.md

@@ -25,6 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - behavioral
 - physiological
 - PET
+- microscopy
 
 # Formatting your data with BIDS
 

mkdocs.yml

@@ -37,6 +37,7 @@ nav:
         - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
         - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
         - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
+        - Microscopy: 04-modality-specific-files/10-microscopy.md
       - Derivatives:
         - BIDS Derivatives: 05-derivatives/01-introduction.md
         - Common data types and metadata: 05-derivatives/02-common-data-types.md

src/02-common-principles.md

@@ -56,6 +56,7 @@ misunderstanding we clarify them here.
     1.  `ieeg` (intracranial electroencephalography)
     1.  `beh` (behavioral)
     1.  `pet` (positron emission tomography)
+    1.  `microscopy`
 
     Data files are contained in a directory named for the data type.
     In raw datasets, the data type directory is nested inside subject and

src/99-appendices/04-entity-table.md

@@ -36,3 +36,7 @@ while entity definitions are in [Appendix IX](09-entities.md).
 ## Behavioral Data
 
 {{ MACROS___make_entity_table(datatypes=["beh"], auxdatatypes=[]) }}
+
+## Microscopy
+
+{{ MACROS___make_entity_table(datatypes=["microscopy"], auxdatatypes=[]) }}

src/schema/objects/entities.yaml

@@ -36,6 +36,15 @@ ceagent:
     with the same label.
   type: string
   format: label
+chunk:
+  name: Chunk
+  entity: chunk
+  description: |
+    The `chunk-<index>` key/value pair is used to distinguish between different
+    regions, 2D images or 3D volumes files, of the same physical sample with
+    different fields of view acquired in the same imaging experiment.
+  type: string
+  format: index
 density:
   name: Density
   entity: den
@@ -294,6 +303,17 @@ split:
     [Scans file](../03-modality-agnostic-files.md#scans-file).
   type: string
   format: index
+stain:
+  name: Stain
+  entity: stain
+  description: |
+    The `stain-<label>` key/pair values can be used to distinguish image files
+    from the same sample using different stains or antibodies for contrast enhancement.
+    Stains or antibodies SHOULD be indicated as appropriate in the `SampleStaining`,
+    `SamplePrimaryAntibodies` and/or `SampleSecondaryAntobodies` keys in the JSON file,
+    although the label may be different.
+  type: string
+  format: label
 subject:
   name: Subject
   entity: sub

src/schema/rules/datatypes/microscopy.yaml

@@ -0,0 +1,46 @@
+---
+# Microscopy
+- suffixes:
+  - TEM
+  - SEM
+  - uCT
+  - BF
+  - DF
+  - PC
+  - DIC
+  - FLUO
+  - CONF
+  - PLI
+  - CARS
+  - 2PE
+  - MPE
+  - SR
+  - NLO
+  - OCT
+  - SPIM
+  extensions:
+  - .ome.tif
+  - .ome.btf
+  - .png
+  - .tif
+  - .json
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    acquisition: optional
+    stain: optional
+    run: optional
+    chunk: optional
+
+- suffixes:
+  - photo
+  extensions:
+  - .jpg
+  - .png
+  - .tif
+  entities:
+    subject: required
+    session: optional
+    sample: required
+    acquisition: optional

src/schema/rules/entities.yaml

@@ -8,6 +8,7 @@
 - acquisition
 - ceagent
 - tracer
+- stain
 - reconstruction
 - direction
 - run
@@ -21,6 +22,7 @@
 - processing
 - space
 - split
+- chunk
 - resolution
 - density
 - label