"Pipeline did not identify any image sets"


This is a very basic technological issue that I have never experienced with CellProfiler before. I am trying to use template that I downloaded straight from your website entitled “Collagen Analysis” on my own images of collagen fibers, but the pipeline will not run. A message says “pipeline did not identify any image sets.” I have attached a screenshot of what my pipeline, image input and warning look like, and my images are clearly inserted. What settings must I change? Thank you!

And here is the pipeline itself, in case the pipeline is the issue:
Collagen Analysis.cp (6.5 KB)


When you click on the module NamesAndTypes >> Files____Does____Contain
Right here we left the “x” letter only to demo, please change it to “Collagen” to fits your purpose.

Also, although it’s not critical, I recommend to filter a bit at Images module, please filter “images only” to prevent the .DS_Store file from being taken.

Hope that helps

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Check the tips in this post


Wow, thank you both for your speedy replies!! This trick worked right away, thank you so much!

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I do have one more question regarding these same collagen images-

Is there a way to quantify a textural analysis of the fibers on CellProfiler, better known as their “Haralick texture features”? I know this technique is common for SHG imaging; can this same form of classification be applied to SEM images of collagen fibers?

Here is an example experiment utilizing this data- http://www.sciencedirect.com/science/article/pii/S1476558616300604

Or how to measure the inter-fiber distances between the fibers?


Yes, we do have MeasureTexture module, measure both object and image texture features .