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Refactor to support multiple BIDS datasets and improve workflow selection

enhancementNew feature or requestNew feature or request

Status: Open.

#73 In khanlab/SPIMprep;

· akhanf opened on Apr 7, 2026

workflow for tif stacks as inputs is out of date

Status: Open.

#69 In khanlab/SPIMprep;

· akhanf opened on Feb 12, 2026

Create a small test dataset and add tests

good first issueGood for newcomersGood for newcomers

Status: Open.

#37 In khanlab/SPIMprep;

· akhanf opened on May 6, 2024

samples.tsv can have duplicates if same samples with different acq flags

Status: Open.

#30 In khanlab/SPIMprep;

· akhanf opened on Apr 4, 2024

Report generation

good first issueGood for newcomersGood for newcomers

Status: Open.

#28 In khanlab/SPIMprep;

· akhanf opened on Apr 3, 2024

Documentation

good first issueGood for newcomersGood for newcomers

Status: Open.

#27 In khanlab/SPIMprep;

· akhanf opened on Apr 3, 2024

Clean-up SPIM JSON file

Status: Open.

#26 In khanlab/SPIMprep;

· akhanf opened on Apr 3, 2024

run bids-validator as a final step

Status: Open.

#25 In khanlab/SPIMprep;

· akhanf opened on Apr 3, 2024

Consider what other minimal pre-processing steps should be included

Status: Open.

#10 In khanlab/SPIMprep;

· akhanf opened on Feb 23, 2024

Make the intensity_rescaling on a per-channel basis

Status: Open.

#5 In khanlab/SPIMprep;

· akhanf opened on Feb 20, 2024