| --- |
| license: mit |
| library_name: halo |
| pipeline_tag: image-segmentation |
| tags: |
| - spatial |
| - xenium |
| - cell-segmentation |
| - cellpose |
| - microscopy |
| - bioimage |
| --- |
| |
| # Halo |
|
|
| Halo is a lightweight pipeline that takes a Xenium dataset folder, builds a 2-channel preprocessing image (DAPI + transcript density), runs Cellpose with the `Halo` pretrained model name, and outputs a cell mask file. |
|
|
| ## Model Description |
|
|
| Halo is a wrapper pipeline around Xenium preprocessing and Cellpose inference. It is intended for whole-image inference without tiling. |
|
|
| ## Intended Use |
|
|
| - Xenium DAPI + transcript density preprocessing |
| - Whole-image cell segmentation using Cellpose |
|
|
| ## Inputs |
|
|
| - Xenium dataset directory containing morphology images and transcript tables |
| - DAPI image auto-detected from `morphology_focus/ch0000_dapi.ome.tif` or `morphology.ome.tif` |
|
|
| ## Outputs |
|
|
| - `halo_processed.tiff` (2-channel DAPI + transcript density) |
| - `cell_masks.npy` (default) or `cell_masks.tiff` |
|
|
| ## Usage |
|
|
| Install (editable): |
|
|
| ```bash |
| pip install -e /hpc/home/xz420/xingyuan/software/Halo |
| ``` |
|
|
| Run: |
|
|
| ```bash |
| halo /path/to/xenium_dataset \ |
| --out-dir /path/to/output \ |
| --mask-format npy |
| ``` |
|
|
| If `--out-dir` is omitted, outputs are written to the current working directory. |
|
|
| ## Parameters |
|
|
| - `--mask-format` set to `npy` or `tiff` |
| - `--processed-out` and `--mask-out` to override output filenames |
| - `--cpu` to force CPU inference |
|
|
| ## Limitations |
|
|
| - Full-image inference can require substantial RAM and GPU memory on large Xenium images |
| - Assumes Xenium coordinate system and transcript columns `x`, `y`, `qv`, and `feature_name` |
|
|
| ## Citation |
|
|
| If you use this pipeline in academic work, please cite Cellpose and Xenium references appropriate to your study. |
|
|
| ## Contact |
|
|
| For questions or improvements, open an issue in the repository. |
|
|
