Path: https://github.com/Image-Py/cellpose-plgs
Version: 0.1
Author: YXDragon, Carsen-Stringer
Email: yxdragon@imagepy.org
Keyword: cellpose, segment, unet
Description: cellpose is a generalist algorithm for cell and nucleus segmentation, this is a cellpose plugin for imagepy.
there are two method to install cellpose-plgs, Install Plugins or use Plugins Manager
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Menus: Plugins > Install > Install Plugins then input https://github.com/Image-Py/cellpose-plgs
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Menus: Plugins > Manager > Plugins Manager, befor you open the manager, you should update the software, (to getting the newest plugins catlog). for git version, please pull, for release version, please use Menus: Plugins > Updata Software.
when the cellpose-plgs is installed seccessfully, The cellpose would appears below the Plugins menus.
Menus: File > Open to Open a Image, you can also use Menus: File > Import > Import Sequence to open a sequence. Then Menus: Plugins > Cell Pose > Cell Pose Eval, you would got a parameter dialog, Setting the parameter, then OK.
Parameters:
model: select model
cytoplasm: select the cytomplasm channel. 0: gray, 1:red, 2:green, 3:blue
nucleus: select the nucleus channel, if there is no, select 0.
show color flow: the color flow result would be shown when checked.
show diams tabel: the diams result would be shown when checked.
slice: process the current image or all images when it is a sequence.
Menus: Analysis > Region Analysis > Geometry Analysis do a region analysis. And we can do many other things in ImagePy, such as set a colormap, or overlay the mask on the original image.
Thanks for CellPose and the supporting from Carsen Stringer and Marius Pachitariu. More detail about CellPose please read the paper or watch the talk.