khanlab / khanlab/SPIMprep

Consider what other minimal pre-processing steps should be included

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Dominant language
Python
Stars
6
Forks
3
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Description

So far only includes flatfield correction (basicpy) and stitching (bigstitcher). Note that stitching with bigstitcher performs intensity rescaling intrinsically. Any other steps to consider?

Contributor guide

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Research direction

Start by reviewing the Snakemake workflow and its existing flatfield correction with basicpy and stitching with BigStitcher. Identify which additional minimal preprocessing steps are appropriate for SPIM data, accounting for BigStitcher's intrinsic intensity rescaling. Done means the preprocessing scope is agreed and the selected steps are specified for implementation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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