Pipeline Incompatible with newer version

Hello,
I am trying to use the Adipocyte Pipeline released by the Rodeheffer Lab (attached) which is designed for Cell Profiler 2.0. I was hoping to be able to use the newer version of Cell Profiler 2.1.1. Whenever I try to run the pipeline in the newest version of Cell Profiler I get various error messages that tend to freeze the program. Any help would be appreciated :smile:

–Elaine
Adipocyte Pipeline numbered Rodeheffer Lab .cp (14.5 KB)

Hi Elaine,

I’m attaching the 2.1.1 version of the 2.0 pipeline I get after importing it. The only items that I needed to change was that a color image is the image type in NamesAndTypes, and that image/object names in the pipeline which have spaces are no longer allowed.

Regards,
-Mark
Adipocyte Pipeline numbered Rodeheffer Lab .cppipe (19.5 KB)

Hey Mark,

I imported your pipeline into the latest CellProfiler version but I am still a bit confused about how to optimize each module (especially the enhance/suppress features & identify primary objects) properly. The purpose for me using CellProfiler is that I want to be able to calculate the cell number and size for each adipocyte. I’ve attached some RGB images that I’ve taken recently.

For the Enhance/Suppress features, the directions for assigning feature size are to move the cursor over the image and look at the pixel intensity under the red channel. When I do this, the intensity ranges from 0.1 to 0.4. From these values how do i determine the feature size since it is orignally listed as 20?

In addition, what part of the current pipeline will allow me to view single cell measurements?

Thank you for your help!



Hello Mark,

Nevermind, the pipeline is able to identify each object accordingly. I also see when you export to spreadsheet how to change it to calculate each image. However, I do have a question about the equation the software uses to convert pixel area into microns (please see my attachment). If I establish a scale whenever I take my pictures, how do I use this data to convert it accordingly. Thank you!

–Chris
Adipocytes.csv (715 Bytes)

Hello,

I am quite new at cell profiler, and I am really interested in this pipeline. However, I have been trying to import it into the program, but it doesn’t seem to be working. When I try to import the pipeline by URL, I get the following error message: “Error while loading None: buffer is too small for requested array”. Then, when I tried to save it as a file, it also keeps failing. Could you tell me what I’m doing wrong or if there is another way to access this pipeline?

Thanks in advance!

It appears that in moving the forum, the links to some of the file attachments were broken. We’re looking into and will get back to you when/if we’re able to fix it.
-Mark

H Mark, I am very interesting in this pipeline. Any website to download, please?
It’s impossible from the forum.
Thanks a lot.