Merge branch 'main' of github.com:hubmapconsortium/ingest-validation-…

…tools into phillips/prevent_multiple_assay_types
hubmapconsortium · Feb 2, 2024 · 3f2022a · 3f2022a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,9 @@
 # Changelog
 
-## v0.0.17 - in progress
+## v0.0.18 (in progress)
+- Update PhenoCycler directory schema
+
+## v0.0.17
 
 - Update atacseq cedar link
 - Add Phenocycler next-gen directory schema
@@ -10,6 +13,12 @@
 - Update PhenoCycler and Histology to 2.2.0
 - Update CEDAR links for PhenoCycler & Histology
 - Refactor Upload to avoid validating the same contributors.tsv multiple times / running plugins over files multiple times
+- Add entry for segmentation-mask
+- Modify directory schema validation such that it takes empty directories into account
+- Add Publication next-gen directory schema
+- Update ATAC/RNA/10X documentation
+- Update Cell Dive documentation
+- Update to support passing list of data_paths to ingest-validation-tests plugins
 
 ## v0.0.16
 

diff --git a/docs/10x-multiome/current/index.md b/docs/10x-multiome/current/index.md
@@ -16,7 +16,7 @@ Related files:
 - [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/10x-multiome/latest/10x-multiome.tsv): Alternative for metadata entry.
 
 
-REQUIRED - For this assay, you must also prepare and submit two additional metadata.tsv files following the metadata schemas linked here for [RNAseq](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq/current/) and [ATACseq](https://hubmapconsortium.github.io/ingest-validation-tools/atacseq/current/).
+REQUIRED - For this assay, you must also prepare and submit two additional metadata.tsv files following the metadata schemas linked here for [RNAseq](https://hubmapconsortium.github.io/ingest-validation-tools/rnaseq/current/) and [ATACseq](https://hubmapconsortium.github.io/ingest-validation-tools/atacseq/current/). For additional documentation on this dataset type, please visit [here](https://docs.google.com/document/d/1cVX_uMA5ehz3TBjrlXSb9KkRo8_5kcFUFhJaWeW9JyU).
 
 ## Metadata schema
 

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -13,7 +13,6 @@ url: "https://hubmapconsortium.github.io" # the base hostname & protocol for you
 markdown: kramdown
 theme: minima
 categories-order:
- - Organ
  - Sample
  - Clinical Imaging Modalities
  - Fluorescence In Situ Hybridization (FISH)
@@ -24,6 +23,7 @@ categories-order:
  - Sequence Assays
  - Single-cycle Fluorescence Microscopy (SFM)
  - Spatial Transcriptomics
+ - Derived Datasets
  - Other TSVs
 
 # Exclude from processing.

diff --git a/docs/atacseq/current/index.md b/docs/atacseq/current/index.md
@@ -16,7 +16,7 @@ Related files:
 - [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/atacseq/latest/atacseq.tsv): Alternative for metadata entry.
 
 
-
+For additional documentation on this dataset type, please visit [here](https://docs.google.com/document/d/1cVX_uMA5ehz3TBjrlXSb9KkRo8_5kcFUFhJaWeW9JyU).
 
 ## Metadata schema
 

diff --git a/docs/celldive/current/index.md b/docs/celldive/current/index.md
@@ -21,7 +21,7 @@ Related files:
 ## Metadata schema
 
 
-<summary><a href="https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2F4b41ed1c-30ae-4a54-839f-9d92750bcc05"><b>Version 2 (use this one)</b></a></summary>
+<summary><a href="https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2F6f9eee7b-7ef1-4f32-a34e-706bbbbb09bf"><b>Version 2 (use this one)</b></a></summary>
 
 
 

diff --git a/docs/codex/current/index.md b/docs/codex/current/index.md
@@ -37,7 +37,7 @@ Related files:
 | <code>extras\/microscope_settings\.json</code> |  | **[QA/QC]** 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. |  |
 | <code>raw\/.*</code> | ✓ | This is a directory containing raw data. |  |
 | <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> | ✓ | OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. 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> |  |
-| <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | This file should describe any processing that was done to generate the images in each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation"  and "is this a channel to use for cell segmentation". |  |
+| <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | This file should describe any processing that was done to generate the images in each channel of the accompanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation"  and "is this a channel to use for cell segmentation". |  |
 | <code>lab_processed\/annotations\/.*</code> |  | Directory containing segmentation masks. |  |
 | <code>lab_processed\/annotations\/[^\/]+\.segmentations\.ome\.tiff</code> |  | The segmentation masks should be stored as multi-channel pyramidal OME TIFF bitmasks with one channel per mask, where a single mask contains all instances of a type of object (e.g., all cells, a class of FTUs, etc). The class of objects contained in the mask is documented in the segmentation-masks.csv file. Each individual object in a mask should be represented by a unique integer pixel value starting at 1, with 0 meaning background (e.g., all pixels belonging to the first instance of a T-cell have a value of 1, the pixels for the second instance of a T-cell have a value of 2, etc). The pixel values should be unique within a mask. FTUs and other structural elements should be captured the same way as cells with segmentation masks and the appropriate channel feature definitions. | lab_processed\/annotations\/.* |
 | <code>lab_processed\/annotations\/segmentation-masks\.csv</code> |  | This file contains details about each mask, with one row per mask. Each column in this file contains details describing the mask (e.g., channel number, mask name, ontological ID, etc). Each mask is stored as a channel in the segmentations.ome.tiff file and the mask name should be ontologically based and linked to the ASCT+B table where possible. The number of rows in this file should equal the number of channels in the segmentations.ome.tiff. For example, one row in this file would ontologically describe cells, if the segmentations.ome.tiff file contained a mask of all cells. A minimum set of fields (required and optional) is included below. If multiple segmentations.ome.tiff files are used, this segmentation-masks.csv file should document the masks across all of the OME TIFF files. | lab_processed\/annotations\/.* |

diff --git a/docs/field-assays.yaml b/docs/field-assays.yaml
@@ -243,6 +243,7 @@ assay_category:
 - Sample Section
 - Sample Suspension
 - Second Harmonic Generation
+- Segmentation Mask
 - Slide-seq
 - Thick Section Multiphoton MxIF
 - Ultrasound
@@ -326,6 +327,7 @@ assay_type:
 - Sample Section
 - Sample Suspension
 - Second Harmonic Generation
+- Segmentation Mask
 - Slide-seq
 - Thick Section Multiphoton MxIF
 - Ultrasound
@@ -839,6 +841,7 @@ is_cedar:
 - Sample Section
 - Sample Suspension
 - Second Harmonic Generation
+- Segmentation Mask
 - Slide-seq
 - Thick Section Multiphoton MxIF
 - Ultrasound

diff --git a/docs/field-schemas.xlsx b/docs/field-schemas.xlsx
diff --git a/docs/field-schemas.yaml b/docs/field-schemas.yaml
@@ -171,6 +171,7 @@ assay_category:
 - scrnaseq
 - scrnaseq-hca
 - second-harmonic-generation
+- segmentation-mask
 - seqfish
 - sims
 - slideseq
@@ -231,6 +232,7 @@ assay_type:
 - scrnaseq
 - scrnaseq-hca
 - second-harmonic-generation
+- segmentation-mask
 - seqfish
 - sims
 - slideseq
@@ -583,6 +585,7 @@ is_cedar:
 - sample-section
 - sample-suspension
 - second-harmonic-generation
+- segmentation-mask
 - seqfish
 - sims
 - slideseq

diff --git a/docs/phenocycler/current/index.md b/docs/phenocycler/current/index.md
@@ -47,6 +47,6 @@ Related files:
 | <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |
 | <code>lab_processed\/images\/.*</code> | ✓ | This is a directory containing processed image files |
 | <code>lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson</code> |  | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
-| <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> | ✓ | OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. 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> |
+| <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> | ✓ | OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling. |
 | <code>lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv</code> | ✓ | 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> |
 
diff --git a/docs/publication/current/index.md b/docs/publication/current/index.md
@@ -28,6 +28,9 @@ Excel and TSV templates for this schema will be available when the draft next-ge
 
 | 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] |
+| <code>data\/.+</code> (example: <code>data/file1.ext</code>) | ✓ | Supplementary data files for the publication. All files referenced by the Vitessce visualization configurations in the vignettes must be included in this directory. |
+| <code>vignettes\/.*</code> | ✓ | Subdirectory containing Vitessce visualization files and a description of those files. |
+| <code>vignettes\/vignette_\d+\/[^\/]+\.json</code> (example: <code>vignettes/vignette_01/file1.json</code>) |  | Vitessce visualization configuration files. One or more visualization configurations can be provided per vignette. |
+| <code>vignettes\/vignette_\d+\/description\.md</code> (example: <code>vignettes/vignette_02/description.md</code>) |  | Description of the vignette and titles for the visualization configuration files. |
 
diff --git a/docs/rnaseq-with-probes/current/index.md b/docs/rnaseq-with-probes/current/index.md
@@ -16,7 +16,7 @@ Related files:
 - [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/rnaseq-with-probes/latest/rnaseq-with-probes.tsv): Alternative for metadata entry.
 
 
-
+For additional documentation on this dataset type, please visit [here](https://docs.google.com/document/d/1cVX_uMA5ehz3TBjrlXSb9KkRo8_5kcFUFhJaWeW9JyU).
 
 ## Metadata schema
 

diff --git a/docs/rnaseq/current/index.md b/docs/rnaseq/current/index.md
@@ -16,7 +16,7 @@ Related files:
 - [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/rnaseq/latest/rnaseq.tsv): Alternative for metadata entry.
 
 
-
+For additional documentation on this dataset type, please visit [here](https://docs.google.com/document/d/1cVX_uMA5ehz3TBjrlXSb9KkRo8_5kcFUFhJaWeW9JyU).
 
 ## Metadata schema
 

diff --git a/docs/segmentation-mask/current/README.md b/docs/segmentation-mask/current/README.md
@@ -0,0 +1 @@
+Moved to [github pages](https://hubmapconsortium.github.io/ingest-validation-tools/segmentation-mask/).
diff --git a/docs/segmentation-mask/current/index.md b/docs/segmentation-mask/current/index.md
@@ -0,0 +1,28 @@
+---
+title: Segmentation Mask
+schema_name: segmentation-mask
+category: Derived Datasets
+all_versions_deprecated: False
+exclude_from_index: False
+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).
+
+For additional documentation on Segmentation Masks, please visit [here](https://docs.google.com/document/d/1TSQon8nTIoyA5bEKxd8IAKYO6nsDabGbbQ8uKN1gj4E).
+
+## Metadata schema
+
+
+<summary><a href="https://docs.google.com/spreadsheets/d/1sMMyKtrxD_PO4TVj0JhOpeLF0fRYe2Fjmxnhp-fNzdM"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30)</a></summary>
+
+
+
+<br>
+
+## Directory schemas
+<summary><a href="https://docs.google.com/spreadsheets/d/1lAGryXYfGIP0jBXjIopB7PtFfo6RqC2bw3RUI4GzTWQ"><b>Version 2 (use this one)</b> (draft - submission of data prepared using this schema will be supported by Sept. 30) </a></summary>
+
diff --git a/examples/plugin-tests/expected-failure/README.md b/examples/plugin-tests/expected-failure/README.md
@@ -1,20 +1,22 @@
 /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/images/faketiff.tiff is not a valid TIFF file: not a TIFF file
 /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/lab_processed/images/Visium_90LC_A4_S1.ome.tiff is not a valid TIFF file: not a TIFF file
+/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/raw/images/faketiff.tiff is not a valid TIFF file: not a TIFF file
+/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/lab_processed/images/Visium_90LC_A4_S1.ome.tiff is not a valid TIFF file: not a TIFF file
+/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2/raw/images/faketiff.tiff is not a valid TIFF file: not a TIFF file
 Threading at 4
 Threading at 4
-Validating matching fastq files in /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1
+Added files from /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1 to dirs_and_files: defaultdict(<class 'dict'>, {PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz')]})})
+Added files from /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2 to dirs_and_files: defaultdict(<class 'dict'>, {PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz')]}), PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz')]})})
+Added files from /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1 to dirs_and_files: defaultdict(<class 'dict'>, {PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz')]}), PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz')]}), PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1'): defaultdict(<class 'list'>, {PosixPath('raw/fastq/RNA'): [PosixPath('/home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz')]})})
+Validating matching fastq file /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
+Validating empty_R_file.fastq.gz...
+    → /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
+Validating matching fastq file /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
 Validating empty_R_file.fastq.gz...
     → /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
-Threading at 4
-Threading at 4
-Validating matching fastq files in /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2
+Validating matching fastq file /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz
 Validating empty_R_file.fastq.gz...
     → /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_A4_S2/raw/fastq/RNA/empty_R_file.fastq.gz
-Threading at 4
-Threading at 4
-Validating matching fastq files in /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1
-Validating empty_R_file.fastq.gz...
-    → /home/gesina/code/ingest-validation-tools/examples/plugin-tests/expected-failure/upload/Visium_9OLC_I4_S1/raw/fastq/RNA/empty_R_file.fastq.gz
 ```
 Plugin Errors:
   Recursively test all ome-tiff files for validity:

diff --git a/src/ingest_validation_tools/directory-schemas/codex-v2.yaml b/src/ingest_validation_tools/directory-schemas/codex-v2.yaml
@@ -25,7 +25,7 @@ files:
   -
     pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
     required: True
-    description: This file should describe any processing that was done to generate the images in each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation"  and "is this a channel to use for cell segmentation".
+    description: This file should describe any processing that was done to generate the images in each channel of the accompanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation"  and "is this a channel to use for cell segmentation".
   -
     pattern: lab_processed\/annotations\/.*
     required: False

diff --git a/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml b/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
@@ -67,7 +67,7 @@ files:
   -
     pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
     required: True
-    description: OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. 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>
+    description: OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. 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>. It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling.
     is_qa_qc: False
   -
     pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
Original file line number	Diff line number	Diff line change
Expand Up		@@ -16,7 +16,7 @@ Related files:
		- [📝 TSV template](https://raw.githubusercontent.com/hubmapconsortium/dataset-metadata-spreadsheet/main/atacseq/latest/atacseq.tsv): Alternative for metadata entry.



		For additional documentation on this dataset type, please visit [here](https://docs.google.com/document/d/1cVX_uMA5ehz3TBjrlXSb9KkRo8_5kcFUFhJaWeW9JyU).

		## Metadata schema

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Expand Up		@@ -21,7 +21,7 @@ Related files:
		## Metadata schema


		<summary><a href="https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2F4b41ed1c-30ae-4a54-839f-9d92750bcc05"><b>Version 2 (use this one)</b></a></summary>
		<summary><a href="https://openview.metadatacenter.org/templates/https:%2F%2Frepo.metadatacenter.org%2Ftemplates%2F6f9eee7b-7ef1-4f32-a34e-706bbbbb09bf"><b>Version 2 (use this one)</b></a></summary>



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		@@ -0,0 +1 @@
		Moved to [github pages](https://hubmapconsortium.github.io/ingest-validation-tools/segmentation-mask/).