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AllenNeuralDynamics / aind-smartspim-stitch

Stitching and fusion pipeline in the cloud
MIT License
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Fix bug when we select a different image resolution in the SmartSPIM stitching package #19

Closed camilolaiton closed 1 year ago

camilolaiton commented 1 year ago

I processed a diSPIM dataset that was imaged with the SmartSPIM machine and the metadata resolution does not match the xyz input resolution I used in the pipeline. Here is the example:

I set the following parameters: X=Y=0.4514 and Z=0.5 um. However, the resolution the neuroglancer link receives in X=Y=1.8 and Z=2.0 um. This should be hardcoded somewhere in the pipeline.

Image

camilolaiton commented 1 year ago

I set the physical pixel sizes to use the import data parameters provided when the stitching is launched and deleted these from the OMEZarr params file.