How to obtain data per well rather than per field-of-view?

cellprofiler

#1

Hello,

I am trying to analyze a high throughput screen using Cell Profiler. For each of my wells, I have twelve images – four fields-of-view and 3 different colors. Is there a way to quantify per well and not per field-of-view (with or without stitching the images)?
Thanks for your help,

Laura


#2

Hi Laura,

Using the pattern of the images name, you can specify Row and Column as Metadata

When you update the Metadata table you can now see a column “Well”.

Then in the module exportToSpreadsheet, select “Add image metadata columns to your object data file”

You can now, group your result per “Well”, using a pivot table in OpenOffiice-Calc or Microsoft-Excel for example.

Best,

Romain


#3

Hi Laura,

Just to add an extra level to what Romain said you can also use your extracted metadata tags in the output file location “Elsewhere” option in ExportToSpreadsheet. This will give you separate directories each with their own CSV in.

image

There’s more information about how to do this here. Just thought that might be of interest.


#4

Thanks for your help @romainGuiet and @lmurphy!!