khanlab/SPIMprep

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A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)

Stars: 6
Forks: 3
Open beginner issues: 0
Indexed issues: 10

Dominant language: Python
License: MIT
Last GitHub push: Apr 7, 2026
Latest indexed: Sep 18, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

10 open issues indexed

Refactor to support multiple BIDS datasets and improve workflow selection Open

enhancement

khanlab/SPIMprep#73 · 1 reaction · 2 assignees · Opened Apr 7, 2026
workflow for tif stacks as inputs is out of date Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

khanlab/SPIMprep#69 · Opened Feb 12, 2026
Create a small test dataset and add tests Open

good first issue

Difficulty 4/5 3-5 days Newbie friendliness 25/100

khanlab/SPIMprep#37 · Opened May 6, 2024
samples.tsv can have duplicates if same samples with different acq flags Open

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

khanlab/SPIMprep#30 · Opened Apr 4, 2024
Report generation Open

good first issue

Difficulty 5/5 Over a week Newbie friendliness 25/100

khanlab/SPIMprep#28 · 1 comment · Opened Apr 3, 2024
Documentation Open

good first issue

Difficulty 4/5 3-5 days Newbie friendliness 30/100

khanlab/SPIMprep#27 · 1 comment · Opened Apr 3, 2024
Clean-up SPIM JSON file Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

khanlab/SPIMprep#26 · Opened Apr 3, 2024
run bids-validator as a final step Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

khanlab/SPIMprep#25 · Opened Apr 3, 2024
Consider what other minimal pre-processing steps should be included Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

khanlab/SPIMprep#10 · 1 comment · Opened Feb 23, 2024
Make the intensity_rescaling on a per-channel basis Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

khanlab/SPIMprep#5 · 1 comment · Opened Feb 20, 2024

khanlab/SPIMprep

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