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
Basics:
Examples:
Reference:
- 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.pretrained_model_ortho
CellposeModel.backbone
CellposeModel.__init__()
CellposeModel.eval()
CellposeModel.eval()
- CellposeDenoiseModel
- DenoiseModel
- SizeModel
- Training
- Metrics
- Flows to masks
compute_masks()
follow_flows()
get_centers()
get_masks_orig()
get_masks_torch()
labels_to_flows()
map_coordinates()
masks_to_flows()
masks_to_flows_cpu()
masks_to_flows_gpu()
masks_to_flows_gpu_3d()
max_pool1d()
max_pool2d()
max_pool3d()
max_pool_nd()
remove_bad_flow_masks()
resize_and_compute_masks()
steps2D()
steps3D()
steps_interp()
- 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.pretrained_model_ortho
CellposeModel.backbone
CellposeModel.__init__()
CellposeModel.eval()
CellposeModel.eval()
SizeModel
get_model_params()
- Cellpose CLI