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visium-no-probes-v3.0.yaml
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visium-no-probes-v3.0.yaml
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files:
-
pattern: extras\/.*
required: True
description: Folder for general lab-specific files related to the dataset
-
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\/[^\/]+\.gpr
required: True
description: This is a 10X Genomics layout file that's generated by 10X and individualized for each Visium slide. This is a text file and can be generated using this 10X web form <https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/slidefile-download> along with the unique 10X Visium slide ID.
is_qa_qc: False
-
pattern: raw\/fastq\/.*
required: True
description: Raw sequencing files for the experiment
-
pattern: raw\/fastq\/RNA\/.*
required: True
description: Directory containing fastq files pertaining to RNAseq sequencing.
-
pattern: raw\/fastq\/RNA\/[^\/]+_R[^\/]+\.fastq\.gz
required: True
description: This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2).
is_qa_qc: False
-
pattern: raw\/images\/.*
required: True
description: Directory containing raw image files. This directory should include at least one raw file.
-
pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|svs|czi|tiff)
required: True
description: Raw microscope file for the experiment
is_qa_qc: False
-
pattern: lab_processed\/.*
required: True
description: Experiment files that were processed by the lab generating the data.
-
pattern: lab_processed\/alignment\.json
required: True
description: JSON file for the manual tissue alignment created using Loupe browser and used as input to Space Ranger.
-
pattern: lab_processed\/images\/.*
required: True
description: Processed image files
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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: lab_processed/images/HBM892.MDXS.293.ome.tiff
-
pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
required: True
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
-
pattern: lab_processed\/images\/[^\/]+\.json
required: False
description: This file is the output from LoupeBrowser, when a data provider manually denotes which spots on the slide contain tissue. This file is optionally used by 10X SpaceRanger.
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pattern: lab_processed\/transformations\/.*
required: False
description: This directory contains transformation matrices that capture how each modality is aligned with the other and can be used to visualize overlays of multimodal data. This is needed to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). In these cases data type may have different pixel sizes and slightly different orientations (i.e., one may be rotated relative to another).
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pattern: lab_processed\/transformations\/[^\/]+\.txt
required: False
description: Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains).
is_qa_qc: False