This script stitches tiled TIFF or IMS images exported from Dragonfly using tile position metadata provided in an associated XML file. It supports z-stack max projection, background subtraction, overlap handling (cropping or blending), and output to TIFF or Zarr.
- Supports TIFF and IMS (Imaris) formats
- Reads tile positions from Dragonfly-generated XML metadata
- Optional Z-axis max projection
- Optional background subtraction
- Handles tile overlaps:
- Crop overlapping regions
- Max-intensity blending of overlaps
- Output to TIFF or Zarr
- Generates a thumbnail preview of the stitched result
Install dependencies with mamba and pip:
mamba install matplotlib tqdm scikit-image python zarr xarray
pip install imaris-ims-file-reader