CellProfilerAnalyst and OMERO

cellprofiler-analyst

#1

We are using the LoadData module in CP to analyse images fetched directly from our OMERO and this is working really well :slight_smile:

What I’d like to find out know is if I could use CPA in the next step and have it connect to our OMERO as well to get the images via “access CellProfiler Analyst images via URL” from the “ExportToDatabase” module in CP.

I don’t plan (yet) to store the database on the OMERO server as well, it could be local for the beginning.

Is this possible to do or could somebody give me a hint on how to set things up? Thanks!


#2

So I tried a bit and here is how far I got:

while the proper URL would have been:
https://omero.biozentrum.unibas.ch/webclient/img_detail/459060/

I have attached my database properties file and my LoadData input csv for reference

plate_581_iids.csv (109.7 KB)
kaistDB.properties (7.3 KB)


#3

Hi,

I’ve opened a feature request to handle this; unfortunately since CPA is maintained almost entirely on a volunteer basis I can’t say for sure if or when someone will get to it. The link to the feature request is probably the best place to stay up to date on the process. Sorry!


#4

thanks for opening the feature request @bcimini!

It feels like at least from getting the URL right it might be fixable more easily, as CPA just seems to take the “image name” from the wrong filed in my input file (plate_581_iids.csv):

There is also a column “Image” in which the proper image numbers are stored, so if CPA would use this one to complete the path then at least the URL to the image on the server would already be correct