Help segmenting bright field images

MouseLand / cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

https://www.cellpose.org/

BSD 3-Clause "New" or "Revised" License

1.24k stars 359 forks source link

Help segmenting bright field images #941

Closed Bassetyabrag closed 1 month ago

Bassetyabrag commented 1 month ago

![Uploading screen9-amoeba-4h-emdm_A1_N_Bf_Processed_1b9605cd-1c68-4ae2-9365-c17ad83229a4.jpg…]() Hello! I am trying to segment brightfield images, such as the one I provided. The problem I am facing is that the cellpose 3 is not able to segment these images correctly. does anyone have any kind of advice on how to segment these kinds of images? Thanks for the help.

Bassetyabrag commented 1 month ago

screen9-amoeba-4h-emdm_A1_N_Bf_Processed_1b9605cd-1c68-4ae2-9365-c17ad83229a4

carsen-stringer commented 1 month ago

you may need to try training a model if the livecell models aren't working for you, check out our info on Cellpose2: https://github.com/MouseLand/cellpose?tab=readme-ov-file#star2-v20-april-2022-star2