Some Questions :)

Hello Guys

Thats my first post here and i started working with Cp today.
I would like to measure the confluency of a cellculture in different time steps. Now, it wasnt a problem to apply my pipeline on my images and it worked great.

I would like to have a percentage of cell coverage ( e.g. 50% confluent), CP does calculate that, but doesnt export it to the spreadsheet in the end, is there any way to include it in the report ?

I do have a good amount of images from each cell culture, is it possible so “show” CP that all images are from one culture and that it should calculate the “overall” confluency ?

I used " identify primaryobjects" which works great. CP shows an image with 3 small pictures (original, cells, cells outline) and a small table with important information. Is it possible to save this exact picture for every analyst image ?

Is there any way to configure CP in a way so that the output folder will always be set inside the source folder ?

  1. Is it possible to write a .bat executable to open CP, load a Pipeline, alternate the Source/Output paths and start the measurements ?

Sorry for all the questions, but iam quite new to this program and some help would be greatly appreciated.



I take it you mean the “% area covered by objects” shown in the window for IdentifyPrimaryObjects? That value is just meant for display, but you can use CalculateMath to produce this value by dividing the AreaOccupied measure (Measurement type: Image, Category: AreaOccupied, Measurement: AreaOccupied) by the total image area (Measurement type: Image, Category: AreaOccupied, Measurement: TotalArea )

CellProfiler processes each image independently of the others, so no, there’s no way to compute an aggregate per-treatment statistic of the type you want. You would need a 3-rd party software package (e.g., Excel) for that.

No, you cannot. However, you can check the “Retain outlines…” box and use OverlayOutlines to overlay the outlines on the original image, and then use SaveImages to save the image overlay out. The per-image counts and thresholds shown in the display window are saved as part of the per-image table in ExportToSpreadsheet.

You can simply set the Default Output Folder to the same location as the Default Input Folder, and make sure that all modules that export results are set to export to the Default Output Folder. However, we generally discourage setting these two locations to the same place since if you’re exporting images, you may end up getting your input and output images mixed up in LoadImages.

You can run CP from command line in “headless” mode, i.e., without the GUI. If you type “CellProfiler.exe --help” from the command line in the installation folder, you will get a list of arguments that you can use into the program, including inputs, outputs, etc. The key one is the -c flag to run “headless”.

Hello mbray

Ok, thank you for all the answers i was looking for :smile:

I used Excel to calculate the %area covert by objects the way you discribed in an excel sheet. I just hoped that this feature mind be inplanted in CP somehow :smile:

The rest of the stuff i am going to try out tomorrow. thank you very much for your fast and complete help.