AllenNeuralDynamics / AllenNeuralDynamics/iSpim-control

Feature Request: processing_manifest.json

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Beschreibung

This feature is requested to help with the goal of automating the upload of iSPIM datasets to the cloud.
The feature requested is the writing of several additional metadata fields pertaining to upload and downstream processing.

A straightforward implementation of this, consistent with other metadata fields, would be a JSON file generated on the rig after/during acquisition. An analogous file written during SmartSPIM acquisition is the _processing_manifest.json_.

This processing metadata file will contain several pieces of important information.

1. Dataset upload status (always "Pending Upload" after acquisition)
2. A list of channels to perform tile alignment (stitching) on
3. A list of channels to perform segmentation on

This format should support the addition of new fields in the future that pertain to processing the datasets.

An example of this processing_manifest.json is included below.

`{

"schema_version": "0.1.0",
"license": "CC-BY-4.0",
"specimen_id": "620642",
"dataset_status": "Pending Upload",
"pipeline_processing": {
"stitching": {
"channel": ["405"]
},
"registration": {
"channels": [
"488"
],
"input_scale": 2
},
"segmentation": {
"channels": ["405", "488"],
"input_scale": "2",
}
}
}
`

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