From 1bb6c1eb0f7b4c8f0f4ab0c882a2e1010b401c8b Mon Sep 17 00:00:00 2001 From: Marie-Helene Bourget Date: Tue, 31 Aug 2021 18:14:15 -0400 Subject: [PATCH 01/28] Add Microscopy chapter in mkdocs.yml --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 34dbb28049..2856ba8c4a 100644 --- a/mkdocs.yml +++ b/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 From 882cdd5f445bc822fa8d581a9981d3663a93b210 Mon Sep 17 00:00:00 2001 From: Marie-Helene Bourget Date: Tue, 31 Aug 2021 18:15:12 -0400 Subject: [PATCH 02/28] Add Microscopy to list of modalities in src/02-common-principles.md --- src/02-common-principles.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/02-common-principles.md b/src/02-common-principles.md index 9143720496..a8fbf69086 100644 --- a/src/02-common-principles.md +++ b/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 From 26ebedf2ddd4dc5b5c3ded9ca762d89a0e8dd1bf Mon Sep 17 00:00:00 2001 From: Marie-Helene Bourget Date: Tue, 31 Aug 2021 18:16:50 -0400 Subject: [PATCH 03/28] Add chunk and stain to src/schema/entities.yaml --- src/schema/entities.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml index 8bcd1a16c1..8e95e0b21a 100644 --- a/src/schema/entities.yaml +++ b/src/schema/entities.yaml @@ -38,6 +38,15 @@ sample: The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset. format: label +chunk: + name: Chunk + entity: chunk + description: | + Chunks refer to multiple regions: 2D images (tiles) or 3D volumes (z-stack) + of the same physical sample (ex: the same slice of tissue under the microscope) + with different fields of view regardless if they overlap or not. + type: string + format: index task: name: Task entity: task @@ -91,6 +100,17 @@ tracer: although the label may be different. type: string format: label +stain: + name: Stain + entity: stain + description: | + The `stain-