Can CellProfiler watch a directory and analyze images as they are created?



Our research group is currently using a proprietary HCA software solution that came with our automated HTP microscope. I am trying to make the case for switching over to CellProfiler due to the more extensive analysis option available and the open nature of the platform. One of the few advantages of our current system is that it performs analysis “on the fly”, so as soon as an image set (all channels) is captured by the instrument, the analysis algorithms for nuclear identification etc are executed on that image set. Our scans (96-well plates) can take around 10h and it is convenient to leave the instrument on over night and then be able to export the single cell csv data files in the morning without having to wait for any image processing to take place.

Currently, CellProfiler would add on ~4-5 hours after the image acquisition step for a typical scan. It would be very convenient if cell profiler could simply watch a directory for new image files and analyze them as they are created. There would naturally be some safety mechanisms in place to prevent from analyzing a file before it is fully written to disk (maybe only analyzing files older than 60 sec or something like that), and then the program would either stop via manually clicking the stop button or after no file has been written to the directory for 10 min or similar.

Is such functionality already available in CellProfiler and if so, how can I use it? If not, are there any plans to add this or can I suggest it somewhere as a future feature?


No, that’s not currently an option in CellProfiler- it processes jobs that are passed to it, it doesn’t have any surveillance capability built in (and my guess is that quite a bit would need to be added to the software to create one). I wouldn’t think it would be that difficult to write a cron job or something similar though to surveil your directories, look for image sets, and dispatch them to CP on the command line though.