cellpose
cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu. For support, please open an issue.
We make pip installable releases of cellpose, here is the pypi. You
can install it as pip install cellpose[gui]
.
You can try it out without installing at cellpose.org. Also check out these resources:
Cellpose3: one-click image restoration for improved cellular segmentation
Cellpose 2.0: how to train your own model
Cellpose: a generalist algorithm for cellular segmentation
paper on biorxiv (see figure 1 below) and in nature methods
twitter thread
Marius’s talk
- Cellpose API Guide
- Cellpose class
- CellposeModel
CellposeModel
CellposeModel.diam_mean
CellposeModel.builtin
CellposeModel.device
CellposeModel.mkldnn
CellposeModel.nchan
CellposeModel.nclasses
CellposeModel.nbase
CellposeModel.net
CellposeModel.pretrained_model
CellposeModel.diam_labels
CellposeModel.net_type
CellposeModel.__init__()
CellposeModel.eval()
CellposeModel.eval()
- CellposeDenoiseModel
- DenoiseModel
- SizeModel
- Training
- Metrics
- Flows to masks
- Image transforms
- Plot functions
- I/O functions
- Utils functions
TqdmToLogger
circleMask()
diameters()
dilate_masks()
distance_to_boundary()
download_url_to_file()
fill_holes_and_remove_small_masks()
get_mask_compactness()
get_mask_perimeters()
get_mask_stats()
get_masks_unet()
get_outline_multi()
get_perimeter()
masks_to_edges()
masks_to_outlines()
outlines_list()
outlines_list_multi()
outlines_list_single()
radius_distribution()
remove_edge_masks()
size_distribution()
stitch3D()
- Network classes
- Core functions
- All models functions
Cellpose
CellposeModel
CellposeModel.diam_mean
CellposeModel.builtin
CellposeModel.device
CellposeModel.mkldnn
CellposeModel.nchan
CellposeModel.nclasses
CellposeModel.nbase
CellposeModel.net
CellposeModel.pretrained_model
CellposeModel.diam_labels
CellposeModel.net_type
CellposeModel.__init__()
CellposeModel.eval()
CellposeModel.eval()
SizeModel
- Cellpose CLI