Cell Segmentation Course
Plugins utilized in the cell segmentation course made by Imaging Scientists in partnership with Chan Zuckerberg Initiative. Segmentation of nuclei, foci in nuclei, and filaments are covered in the course, which you can work through here: https://chanzuckerberg.github.io/napari-segmentation-workshop/intro.html.
Dannielle McCarthyApplications Scientist,Chan Zuckerberg Initiative
Collection last updated: 07 November 2022
a generalist algorithm for anatomical segmentation
Utilize CellPose with FIJI to complete the first cell segmentation workflow: https://chanzuckerberg.
PartSeg is python GUI and set of napari plugins for bio imaging analysis especially nucleus analysis,
Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Paweł Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczyński
Utilize PartSeg with napari-segment-blobs-and-things-with-membranes to complete the second cell segm...
A plugin based on scikit-image for segmenting nuclei and cells based on fluorescent microscopy images with high intensity in nuclei and/or membranes
Utilize napari-segment-blobs-and-things-with-membranes with PartSeg to complete the second cell segm...
A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science
Allen Institute for Cell Science
Utilize napari-allencell-segmenter to complete the third cell segmentation workflow: https://chanzuc...