From a36accfba2cddf6a80d9ec1f471c6c7d9058e873 Mon Sep 17 00:00:00 2001 From: j-uranic <117292295+j-uranic@users.noreply.github.com> Date: Thu, 21 Mar 2024 09:53:44 -0400 Subject: [PATCH 1/3] Update histology-v2.yaml Add qptiff to /raw/images/ --- src/ingest_validation_tools/directory-schemas/histology-v2.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ingest_validation_tools/directory-schemas/histology-v2.yaml b/src/ingest_validation_tools/directory-schemas/histology-v2.yaml index d11b1d59a..684117d41 100644 --- a/src/ingest_validation_tools/directory-schemas/histology-v2.yaml +++ b/src/ingest_validation_tools/directory-schemas/histology-v2.yaml @@ -22,7 +22,7 @@ files: required: True description: Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file. - - pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff) + pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff) required: True description: Raw microscope file for the experiment is_qa_qc: False From 172cab3ae2b9ae94f3d7947a82d9e2bcee446f83 Mon Sep 17 00:00:00 2001 From: j-uranic <117292295+j-uranic@users.noreply.github.com> Date: Thu, 21 Mar 2024 09:54:19 -0400 Subject: [PATCH 2/3] Update CHANGELOG.md Update Histology directory schema --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7578d64c4..ecc4341c7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ - Update Histology with links - Update GeoMx NGS directory schema - Ported murine from SenNet +- Update Histology directory schema ## v0.0.17 From 4f501b36bcb11a2038863bffd33504213089f0f3 Mon Sep 17 00:00:00 2001 From: Juan Puerto <=> Date: Thu, 21 Mar 2024 09:57:37 -0400 Subject: [PATCH 3/3] Docs: Update histology docs --- docs/histology/current/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/histology/current/index.md b/docs/histology/current/index.md index 00c48f36e..37a3780db 100644 --- a/docs/histology/current/index.md +++ b/docs/histology/current/index.md @@ -37,7 +37,7 @@ Related files: | extras\/microscope_settings\.json | | **[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 if help is required in generating this document. | | | raw\/.* | ✓ | Raw data files for the experiment. | | | raw\/images\/.* | ✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file. | | -| raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff) | ✓ | Raw microscope file for the experiment | | +| raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff) | ✓ | Raw microscope file for the experiment | | | lab_processed\/.* | ✓ | Experiment files that were processed by the lab generating the data. | | | lab_processed\/images\/.* | ✓ | Processed image files | | | lab_processed\/images\/[^\/]+\.ome\.tiff (example: lab_processed/images/HBM892.MDXS.293.ome.tiff) | ✓ | OME-TIFF files (multichannel, multi-layered) produced by the microscopy 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. | |