.cp file is not being recognized on my system

Hi,

I am new to using CellProfiler and started attempting to use CellProfiler for my IHC images 2 days ago but had some problems as stated below;

Primarily my pipeline file in my default input folder doesn’t look active (its icon appears as a white square) and I when I click to open it, my system says windows cannot open this file and further ask if it should check the internet for a suitable programme to open it. I am using a Windows 7 operating system.

1.“Now that you have loaded an example pipeline, press the ‘analyze images button’ to access and process a small image from the cellprofiler website so you can see how the CellProfiler works”
2. When i click the analyze images button, it states “Pipeline processing finished, no images taken”
So I created my own pipeline using loadimages, identifyprimaryobjects, identifysecondaryobjects, identifytertiaryobjects
and converted the cloured IHC to grey scale (using corel paintshop) but I cannot analyze/count the image for the stained cells.

Can you help please? Kindly use simple technical languages so I can understand what you are explaining.

Thank you.

Tom




Hi Tom,

Glad you found CellProfiler!

You’re not doing anything wrong; double-clicking on a pipeline (.cp) file is not expected to launch CellProfiler. (There are a few reasons for this, but in any case, in the next version we have changed how we save projects and so it should work.) Instead, launch the CellProfiler application and then choose File -> Load pipeline.

[quote]1."Now that you have loaded an example pipeline, press the ‘analyze images button’ to access and process a small image from the cellprofiler website so you can see how the CellProfiler works"
2. When i click the analyze images button, it states “Pipeline processing finished, no images taken”[/quote]

I was confused at first, but this is our error! We are in the process of updating our software and example pipelines, and in fact the “load a simple pipeline” link that you clicked was recently changed to point to a new file. This should have populated a new pipeline for you, but it doesn’t (eek!). We’ll fix this today – thanks for reporting this!

[quote]So I created my own pipeline using loadimages, identifyprimaryobjects, identifysecondaryobjects, identifytertiaryobjects
and converted the cloured IHC to grey scale (using corel paintshop) but I cannot analyze/count the image for the stained cells.[/quote]

It sounds like you’re on the right track. But other users have similar issues (i.e. IHC), so please search the Forum here and you’ll find similar histological projects, like:

cellprofiler.org/forum/viewtopic … logy#p9907

cellprofiler.org/forum/viewtopic … ylin#p9772

Generally, I’d suggest following the suggestions in the thread here, but also note that you shouldn’t pre-process in any other software (e.g. corel) – use CellProfiler’s UnmixColors module instead which utilizes the color information in the image.

But finally note that histological slides can be troublesome relative to fluorescent cells in vitro. The background can vary a lot, especially from sample-to-sample. If the CP approach is painful, you might also try a pixel classifier called ilastik that interacts well with CP.

Cheers,
David

Thank you David,

I will try again and follow your suggestions as you have adviced.

Thank you once again.

Regard,

Thompson