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ExaScience / process-plate

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How to use these script files？ #1

Open zhouhao-learning opened 6 years ago

zhouhao-learning commented 6 years ago

I found this link in your paper. You gave a link to CellProfiler, but I found it to be a piece of software. I don't know how to use these script files. Can you have a specific example or description?

roelWuyts commented 6 years ago

Hello, CellProfiler is software developed by the Broad to analyze images. To do this you create a pipeline of image processing steps. Once you have this pipeline you may need to apply this pipeline to many (thousands) of plates from high content imaging experiments, like we had to do in the mentioned paper. We therefore created some simple scripts to help with this and open-sourced them for reference. Useage and functionality are pretty simple: you invoke it with a directory that contains a plate worth of images (or with subdirectories per plate) and it will run through these. We provided the pipelines we used and some corresponding steps. You will likely have to adapt this to your particular pipelines or steps, and possible naming conventions for the image files. These scripts are only a first step. We will soon release an update of this that is much improved. I am not sure this answered your question. If not, feel free to be more specific.

zhouhao-learning commented 6 years ago

@roelWuyts Thank you. I'll try to use it as you said. I looked at the Processplate. sh script file you provided. I found a python file in it: . / CellProfiler / CellProfiler. py, but I didn't find this file in this project. Where should I get this file?

roelWuyts commented 6 years ago

Dear, I just had a look and in the meantime the latest CellProfiler is Cellprofiler 3, which is indeed different. We used CellProfiler 2.1.1 (also the provided pipelines were used with this version, I do not know if they work with CellProfiler 3). This should do the trick: git clone https://github.com/CellProfiler/CellProfiler.git git -C ./CellProfiler checkout -b 2.1.1 tags/2.1.1 You then have the expected CellProfiler.py. Hope this helps !

zhouhao-learning commented 6 years ago

@roelWuyts Thank you. Your method is right.