angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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rescale_factor not affecting segmentation #1001

Closed ngreenwald closed 1 year ago

ngreenwald commented 1 year ago

Please refer to our FAQ and look at our known issues before opening a bug report.

Describe the bug The rescale_factor parameter in the segmentation notebook should dictate how images are processed by the model. However, Candace was experimenting with new imaging settings, and found that it wasn't working as intended.

Expected behavior Modifying this variable should result in dramatically different segmentation quality based on the value provided.

To investigate the problem, we should first check if 1) the value set in the notebook is actually being submitted to the server, and 2) compare the segmentation output when we specify a given rescale factor, compared with manually rescaling the image by the same factor and then submitting the image.