image-py / cellpose-plgs

cellpose plugin for imagepy

cellpose-plgs

Path: https://github.com/Image-Py/cellpose-plgs

Version: 0.1

Author: YXDragon, Carsen-Stringer

Email: [email protected]

Keyword: cellpose, segment, unet

Description: cellpose is a generalist algorithm for cell and nucleus segmentation, this is a cellpose plugin for imagepy.

Document

Install

there are two method to install cellpose-plgs, Install Plugins or use Plugins Manager

1. Menus: Plugins > Install > Install Plugins then input https://github.com/Image-Py/cellpose-plgs

   

2. 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.

Usage

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.

Analysis

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.

Reference

Thanks for CellPose and the supporting from Carsen Stringer and Marius Pachitariu. More detail about CellPose please read the paper or watch the talk.

cellpose-plgs's Issues

Batch process with script version using cellpose plgs

Dear ImagePy team,

I knew ImagePy has a very user-friendly UI. But, given the cellulose computation is time-consuming. Often time, we have to wait for 5-10 minutes to process one image. So, I think the batch process many images overnight will be very helpful. If we had a working pipeline, e.g., cellpose segmentation --> imagery geometry analysis --> export the coordinate of the mask for each channel into either Pandas or Numpy, I wonder how to use the script to do it? or is there anything that ImagePy can handle in the UI? We are really looking forward to seeing a way to achieve this.

Thank you,

My cellpose Doesn't seem to work

First, I don't have any idea of programming.
Said that when i run the cellpose plugin in my imagepy says "Module not Found Error: No module named 'cellpose' "
I haven't seen that as a common error.
Am I missing something to install ?

TypeError when I use plugins manager

When I try to explore the plugin using plugin manager. The manager window looks strange and I saw a error message:

how to enable CUDA in the plugins

Dear ImagePy team,

I came from cellpose repository and I am a cellpose user. When I use cellpose, I can select CPU or GPU to compute the segregation. But, I didn't see this option here. The another question is when I install cellpose-plgs from imagePy. I saw mxnet and mxnet-mkl was installed. But, my CUDA version is 10.1. If I use cellpose alone, I should install mxnet-cu101. Can you give me some suggestions?