Several Questions in terms of Usuage



To Whom This May Concern,

I am a newbie at the CellProfiler Software. I have a few questions that I am hoping to get answered.

  1. How do you upload an image onto the CellProfiler? I attempted to do it once; however, I do not remember exactly how I did it and when I did it, I think I did it incorrectly.

  2. Once the image is on the CellProfiler, how do you analyze it? Again, with the image that I had attempted to upload - I would double click on the image under the list titled “Authors,” and it would open up into a seperate window. Is this what is supposed to happen? I thought that it should all be on the one window, which has the “Modules List,” the “pixel size,” etc.

  3. **Once you get the image onto the CellProfiler, how do you add the different tools to the Modules List to use? **I added numerous ones to the pipeline, for instance “GraytoColor.” Now, how do you apply this module to the actual image?
    Again, I am very new at this and these are pretty basic questions. If someone could please respond and go through the step by step process on how to analyze your image, that would be great!

Thank you,


Hi Chelsea,

Thanks for giving the program a try!

If you’re completely new to using CellProfiler, I highly recommend checking out our Examples page. Here, you’ll find some sample images which you can download, as well as a pipeline for each image set (a pipeline is a set of modules which you use to analyze an image set).

Scroll down to the “How do I get started?” section, where you’ll find a brief summary on how to make the best use of the example images and pipelines. If you follow the procedure outlined there, it should help address the questions you posed. And of course, if you’re still stuck, you can post again in the forums.

Hope this helps,