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CaroAMN merged 1 commit into from
Feb 13, 2026
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update README for new workflow #49

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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -34,13 +34,13 @@ The pipeline consists of 3 major components: Preprocessing, Cell-Nuclei quantifi

**Preprocessing**

This stage reconstructs the 3D image from raw light-sheet data. Here two different workflows can be chosen:
This stage reconstructs the 3D image from raw light-sheet data. Here three different workflows can be chosen:

1. `align_stitch` for multi-channel brain images: \
Performs intensity adjustment, channel alignment, and iterative tile stitching
1. `int_align_stitch`: Performs intensity adjustment, channel alignment, and iterative tile stitching

2. `stitch` for single-channel images: \
Performs intensity adjustment and interactive tile stitching.
2. `int_stitch`: Performs intensity adjustment and iterative tile stitching.

3. `stitch_only`: Performs only iterative tile stitching

**Allen Brain Atlas Registration (Optional)**

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