I want to analyze multiple sets of images using CellProfiler2.1.1 Windows version. And I note that the CreateBatchFiles module may help to solve the large jobs. But I am ignorant of the setting of this module. There are some fundamental problems:
- I cannot find the corresponding Linux version in the developer’s webpage(https://cellprofiler.org/previous_releases/). But I found some topics of the CellProfiler2 Linux version installation (https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)) and it seems fuzzy of how to fetch and install a CellProfiler2.1.1 or later version. Do I need to install the corresponding version in the server ? And are there any dependencies changes of the version?
- Since the file path in cluster computer is written as the format ‘/server_name/your_name/your_data/images’, I am misunderstanding with the ‘server_name’ format. Is there any linux command can I get the right format or does this contains the IP of the server?
- Since the images are stored on my local computer, but the inputs are finally processed by the remote server and the output are stored on the local computer. I am confused with this file path setting and the problem of online job processing. My server manages jobs by qsub system so I should submit the job in a PBS script.
- In the ClassifyPixels process, the images were classified by a .h5 file (~90 Mb in size) produced from ilastik. But I am ignorant of how to write the command line with this input.
What do you think of that? Cheers for the detailed answer:smile: