Cannot download pipeline examples

Hi:

I’ve been trying to download the examples you have to compare with the pipeline I’m creating but I can’t. Is there any requirements to download them? I’m trying to count nuclei (very basic) but the program splits some nuclei counting 2 instead of 1.

Pipeline is very simple:
load images
identify primary object
measure object intensity
export to spreadsheet

I just started today to try to use the program so most likely I’m doing it wrong…if I could check the examples I’m sure I could do better.

Thanks for your help!

Hi there,

Could you clarify exactly what problem you’re having with downloading the example pipelines? For example, when you click here:
cellprofiler.org/linked_files/Ex … Images.zip

does it download the .zip file to your computer? Then, have you unzipped it and loaded the pipeline (the .cp file) into CellProfiler using File > Load Pipeline?

To answer your specific question, if nuclei are being erroneously split into two, the settings in IdentifyPrimaryObjects need adjustment. Check the help for the various settings (especially those related to de-clumping). If you’re still having trouble, feel free to post example images and the pipeline you’ve developed so far.

Anne

Dear Anne,

I also cannot download a pipeline example. The pipeline (“2011_06_06.cp”) is under the topic titled “Stomata and pavement cell counting”.

When I click on the link, a new Firefox window opens, with the following address: http://forum.image.sc//upload-forum-cellprofiler-org.s3-us-west-2.amazonaws.com/original/2X/4/4f4f7baff870a32162472ee8056809de0466be4d.cp
However, nothing shows up in the window. I am, however, able to download example pipelines from the website.

Thank you in advance,
wmolenaar

Hi Anne,

I’m experiencing a similar issue with pipelines posted on this forum, but not the example pipelines contained in .zip files.

Best,
Sebastian

Maybe the problem is the forum doesn’t allow the new file extension, as detailed in this thread?

I cannot download 2 different .cp files but I can download the .cppipe pipeline here.

I added a Github issue for this download issue. .cp and .cpproj and many other file types are now ok to upload, so that’s not the issue (not directly, at least). I’m pretty sure it is only pipelines and some other file types that were on our old forum which somehow during the migration process to our new Discourse forum a month+ ago got messed up or otherwise marked as not able to download. We’ll look into it further, as this is annoying for many. Thanks

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See this for a little more info: Cannot download old pipelines