"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


Check the tips in this post


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


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 .