Releasing #cellpose, a generalist algorithm for cellular segmentation. Try it now directly on the website cellpose.org, install the code package github.com/MouseLand/cell…, read the preprint biorxiv.org/content/10.110… or watch the talk .
We developed Cellpose as a generalist algorithm, because many small and big problems in biology require cell segmentation, and there just isn’t enough time to write a new pipeline for every type of data. 
We trained Cellpose on a diverse set of 608 images, collected and segmented by us. See the t-SNE plot of image styles below.
Out-of-the box, Cellpose can segment a large variety of images from different types of microscopy, different tissues and different stains or fluorescent tags. It can even segment rocks, jellyfish and sea urchins.
The GUI lets you manually segment your own images at a speed of 300-600 objects per hour. Cellpose doesn’t need super precise outlines.
Send us your manual segmentations and we’ll include them in the next Cellpose release, making the model better for yourself and everyone else!
Check out the preprint for much more: nucleus segmentation, comparisons to previous state-of-the-art methods, a cell size prediction network etc biorxiv.org/content/10.110…
