Cells distribution inside wells

[Ahmed (Ahmed Alsaeedi)]

Hi people,
I’m brand new with cell profiler. I just started to use it last week. I have Cell Voyager 600 images. The images are annotated with plate, well, and field name. The CP analyst gives me the total cell number per image. I would like to have the total number per well and per field as well. I’m using PBMCs and interested to study cell distribution inside the well after seeding.
Thanks

[Alison_Kozol]

Hi Ahmed -

Thanks for giving CellProfiler and CellProfiler Analyst a try! I highly recommend that you visit our “Before Posting: Tips page” (link below). This will optimize your post so that we can best assist you.

Before Posting: Tips

Use the Search function (magnifying glass at the upper-right corner) to see if other users have asked the same question and received an answer Browse the FAQ If you create a new topic, please attach to your post: A description of the phenotype of interest, i.e, the cellular image features that you are looking for. Not all of your readers will be fluent in the details of your biological system or assay. A basic, novice-level description goes a long way to making sure that others understand you…

All the best,
Alison

[David_Logan]

Hi Ahmed,

Open your CPA properties file and look at the section called (Dynamic) Groups. You’d need something like this (which you can also specify in ExportToDatabase so you don;t need to edit the properties file)

group_SQL_Well = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Per_Image_Table.well FROM Per_Image_Table

Hope that helps, but otherwise like Alison says, please post more info here like the pipeline file, properties file, etc.

[Ahmed (Ahmed Alsaeedi)]

Hi David
Thanks for your reply. I will have a look and let know.
Best
Ahmed

[Ahmed (Ahmed Alsaeedi)]

Hi David,
Its working. Now I have my cells number per well!
Thanks
Ahmed