General: Release MERFISH (#1344)

* General: Release MERFISH * Update merfish-v2.0.yaml Add MERFISH directory schema * Update CHANGELOG.md * General: Update MERFISH docs. --------- Co-authored-by: Juan Puerto <=> Co-authored-by: j-uranic <[email protected]>
hubmapconsortium · Jul 12, 2024 · d85df0c · d85df0c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## v0.0.24 (in progress)
+- Release MERFISH
+- Add MERFISH directory schema
+
 ## v0.0.23
 - Add token to validation_utils.get_assaytype_data, replace URL string concatenation with urllib
 

diff --git a/docs/merfish/current/index.md b/docs/merfish/current/index.md
@@ -1,33 +0,0 @@
----
-title: MERFISH
-schema_name: merfish
-category: Fluorescence In Situ Hybridization (FISH)
-all_versions_deprecated: False
-exclude_from_index: True
-layout: default
-
----
-
-Related files:
-
-Excel and TSV templates for this schema will be available when the draft next-generation schema, to be used in all future submissions, is finalized (no later than Sept. 30).
-
-[This link](https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0) lists the set of fields that are required in the OME TIFF file XML header.
-
-## Metadata schema
-
-
-<summary><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) (TBD)</summary>
-
-
-
-<br>
-
-## Directory schemas
-<summary><b>Version 2.0 (use this one)</b></summary>
-
-| pattern | required? | description |
-| --- | --- | --- |
-| <code>TODO</code> | ✓ | Directory structure not yet specified. |
-| <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. [Exists in all assays] |
-

diff --git a/src/ingest_validation_tools/directory-schemas/merfish-v2.0.yaml b/src/ingest_validation_tools/directory-schemas/merfish-v2.0.yaml
@@ -1,9 +1,86 @@
 files:
   -
-    pattern: 'TODO'
-    description: 'Directory structure not yet specified.'
+    pattern: extras\/.*
     required: True
+    description: Folder for general lab-specific files related to the dataset.
   -
-    pattern: extras\/.*
+    pattern: extras\/microscope_hardware\.json
+    required: True
+    description: A file generated by the micro-meta app that contains a description of the hardware components of the microscope. Email HuBMAP Consortium Help Desk <[email protected]> if help is required in generating this document.
+    is_qa_qc: True
+  -
+    pattern: extras\/microscope_settings\.json
+    required: False
+    description: A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <[email protected]> if help is required in generating this document.
+    is_qa_qc: True
+  -
+    pattern: raw\/.*
+    required: True
+    description: All raw data files for the experiment.
+  -
+    pattern: raw\/additional_panels_used\.csv
+    required: False
+    description: If multiple commercial probe panels were used, then the primary probe panel should be selected in the "oligo_probe_panel" metadata field. The additional panels must be included in this file. Each panel record should include:manufacturer, model/name, product code.
+  -
+    pattern: raw\/gene_panel\.csv
+    required: True
+    description: The list of target genes.
+  -
+    pattern: raw\/custom_probe_set\.csv
+    required: False
+    description: This file should contain any custom probes used and must be included if the metadata field "is_custom_probes_used" is "Yes". The file should minimally include:target gene id, probe seq, probe id. The contents of this file are modeled after the 10x Genomics probe set file (see <https://support.10xgenomics.com/spatial-gene-expression-ffpe/probe-sets/probe-set-file-descriptions/probe-set-file-descriptions#probe_set_csv_file>).
+  -
+    pattern: raw\/micron_to_mosaic_pixel_transform\.csv
+    required: False
+    description: Matrix used to transform from pixels to physical distance.
+  -
+    pattern: raw\/manifest\.json
+    required: True
+    description: This file contains stain by channel details and pixel details.
+  -
+    pattern: raw\/codebook\.csv
+    required: True
+    description: CSV containing codebook information for the experiment. Rows are barcodes and columns are imaging rounds. The first column is the barcode target, and the following column IDs are expected to be sequential, and round identifiers are expected to be integers (not roman numerals).
+  -
+    pattern: raw\/positions\.csv
+    required: True
+    description: File that includes the top left coordinate of each tiled image. This is required to stitch the images.
+  -
+    pattern: raw\/dataorganization\.csv
+    required: True
+    description: Necessary image definitions
+  -
+    pattern: raw\/[^\/]+\.DAX
+    required: True
+    description: The raw image stack.
+  -
+    pattern: raw\/images\/.*
+    required: True
+    description: Directory containing raw image files. This directory should include at least one raw file.
+  -
+    pattern: raw\/images\/[^\/]+\.tif
+    required: True
+    description: Raw microscope file for the experiment.
+  -
+    pattern: lab_processed\/.*
+    required: True
+    description: Experiment files that were processed by the lab generating the data.
+  -
+    pattern: lab_processed\/detected_transcripts\.csv
+    required: True
+    description: A file containing the locations of each RNA target.
+  -
+    pattern: lab_processed\/images\/.*
+    required: True
+    description: Processed image files
+  -
+    pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
+    required: True
+    description: OME-TIFF files (multichannel, multi-layered) produced by the microscopy experiment. If compressed, must use loss-less compression algorithm. For Visium this stitched file should only include the single capture area relevant to the current dataset. For GeoMx there will be one OME TIFF file per slide, with each slide including multiple AOIs. See the following link for the set of fields that are required in the OME TIFF file XML header. <https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0>
+    is_qa_qc: False
+    example: HBM892.MDXS.293.ome.tiff
+  -
+    pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
     required: True
-    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]
+    description: This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0>
+    is_qa_qc: False
diff --git a/src/ingest_validation_tools/table-schemas/assays/merfish-v2.yaml b/src/ingest_validation_tools/table-schemas/assays/merfish-v2.yaml
@@ -1,4 +1,3 @@
-exclude_from_index: True
 description_md: '[This link](https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0) lists the set of fields that are required in the OME TIFF file XML header.'
 draft: true
 fields: