Images from tile scanning of each well on a 24well plate?

Dear all,

I’m running some tile-scan imaging experiments on a 24well labtek chamber plate with 20x objective. I’ve set up my microscope to scan a ROI in each well consisting of 6 tiles (a 2 by 3 tile scan in this well), therefore it is a multi-tile in a multi-well plate imaging experiment. For example, at well A3 tile 6, the file name I give it to each image is the following: DAPI-Well-A-3-Xpos2-Ypos3; at well B2 tile 2, the file name I give it to each image is DAPI-Well-B-2-Xpos2-Ypos1; However, it seems that Cellprofiler does not quite like that naming syntax to perform analysis of all my images.

I noticed that Cellprofiler can perform analysis on a 96well plate HCS experiment, but the examples only have one image per well. My case is similar but slightly different since I have multiple tiles in each well. Therefore, I wonder if Cellprofiler support analysis on that, if yes, how I can rename my images in a way that can be correctly identified by cellprofiler to construct a pipeline.

Thank you.


Er Liu
Postdoc Scientist
La Jolla Bioengineering Institute
San Diego, 92121

Hi Er,

You mention that “Cellprofiler does not quite like that naming syntax.” Can you give more details on what you mean by this? Are you running into an error of some sort, or something else? Also, what image format are you using? Based on your description, it seems like CellProfiler should be able to handle the assay…


Hi, Mark,

I think I should make my question clearer. What I want to do is to perform cell profiler analysis on a multi-tile scaning of a 24 well plate dataset, and export the results into FCS Express Image Cytometry (De Novo software). Therefore, I want to know the correct naming criteria for multi-field of view in multi-well plate format dataset. Now this question has been addressed by Sean (De Novo software).

Thanks for your help.


Hi Er,

Would you mind posting the answer you got from Sean, so others can refer to it if they have the same question?

Hi Er and Mark,
There is now some documentation, as well as a tutorial and sample pipeline, on the De Novo Software website at … le_fie.htm. This covers the name format that one should use for exporting multiple wells with multiple fields of view per well from CellProfiler to FCS Express Image Cytometry.