Mulit-image tiff input

This is my first attempt at using cell profiler, so I do not know much about its use. I do lots of work with Fiji, so that is the paradigm I know.
I am now attempting to reproduce something which i wrote in FIji, using cell profiler.

I am using the speckle detection pipeline example, and have it working on my images.
However, my images (after some preprocessing done in Fiji) exist as mulit-TIFF image stacks. So I have a single TIFF file with 10 images (from 10 fields) of speckles, and a second multi-Image TIFF with 10 images of dapi stained nuclei.

My problem is that I want the speckle detection pipeline to run on all 10 image, and it only runs on the first image in the stack.
I suppose that I can rewrite the multi-image TIFFs as individually sequentially numbers images in a directory. I hope that there is a better way (like the imageJ stacks that I know and love).

I also want to know how to do flow control (loops, conditionals, etc) in a pipeline.

Thanks in advance – sorry if these beginner’s questions should have been obvious.


I found the answer in the loading images section of the manual. First time through, I had not scrolled far enough down, and only saw the part about files with individual images. I needed to lick on the update button below the divider, and not just the update metadata button in the top part. Sorry about that.

Next challenge is to see if I can find a way to overlay the marked telomeres on the the original image so that I can see if the result makes sense.

Hi Aryeh,
Thanks for giving CellProfiler a try!

To answer this question: There is no flow control as such: pipelines are completely linear in execution. All modules rely on upstream inputs and feed their results exclusively downstream. The one exception that comes to mind is the FlagImage module, which can skip the remainder of a pipeline if a particular condition is met, based on upstream values/measurements. But that’s a rather special case…

Thank you for your response.

Can I set this forum so that I receive all posts as email (not just replies to my posts)?

Unfortunately, no.

Though note that you can “Subscribe” to each subforum, which you can have email you if a new post occurs (only once though, afaik). It’s not great, but it’s better than nothing. Navigate to each subforum and then at the very bottom of the page you should see a “Subscribe” link to click on.