Feature/ng link - Githubissues

AllenNeuralDynamics / aind-smartspim-stitch

Stitching and fusion pipeline in the cloud

MIT License

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Feature/ng link #3

Closed camilolaiton closed 1 year ago

camilolaiton commented 1 year ago

In this branch I have implemented the following principal feature:

Generation of neuroglancer links when the computation is performed in the cloud. It creates a .txt file with the link and a .json file with neuroglancer configuration in the stitched output folder in a google bucket.

Also, I have added the following:

Downscaling metadata in OMEZarr .zattrs
Updating repository for documentation in Sphinx
Updating Dockerfile for CodeOcean (Can work in GCP but I'm figuring out how to use it in Cloud Run with gcsfuse)
Fix OMEZarr conversion when stitching single channel

dyf commented 1 year ago

Thinking about it a bit, I'm wondering if you want ng_link to worry about output files at all. Maybe it's job is just to generate links, and the rest of your module can worry about where they go.