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haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
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Multimodal test #107

Closed dannda closed 1 year ago

dannda commented 1 year ago

Issue using ome_zarr.writer.write_image where downsampled images are applied a gaussian filter even when explicitly setting nearest method for scaler.

edit: couldn't find out what caused the filter; switched to using write_multiscales which requires adding offset to all zarr levels

dannda commented 1 year ago

Finding issues with environment.yaml with python==3.9 (as in docker requirements). Environment works with python3.10