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desi-v2.yaml
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desi-v2.yaml
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files:
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pattern: extras\/.*
required: True
description: Folder for general lab-specific files related to the dataset.
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pattern: extras\/mass-spec_environment\.(?:json|tsv)
required: False
description: JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that's used to describe the imaging equipment.
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pattern: raw\/.*
required: True
description: Raw data files for the experiment.
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pattern: raw\/imzML\/.*
required: True
description: Raw mass spec data.
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pattern: raw\/imzML\/[^\/]+\.ibd
required: True
description: Mass spec data saved in a binary format.
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pattern: raw\/imzML\/[^\/]+\.imzML
required: True
description: Mass spec metadata saved in XML format. Index to .ibd file.
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pattern: lab_processed\/.*
required: True
description: Experiment files that were processed by the lab generating the data.
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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. 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
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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>
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pattern: lab_processed\/transformations\/.*
required: False
description: Directory containing image transformations.
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pattern: lab_processed\/transformations\/[^\/]+\.txt
required: False
description: Transformations/map back to autofluorescence microscopy (related) data
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pattern: lab_processed\/annotations\/.*
required: True
description: Directory containing annotations
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pattern: lab_processed\/annotations\/[^\/]+_MolecularAssignments\.tsv
required: True
description: TSV file containing the m/z, molecular assignment, etc.