Cellprofiler analyst

Hi, I want to upload my own pictures on cell profiles analyst program to be able to learn the program which cell shapes with special appearance I am interested in. Unfortunately do not know how to do it. Hope you can explain it to me?

Hi @Navid,

In order to learn the CellProfiler Analyst software, I recommend starting with the Translocation tutorial available on our github page: https://github.com/CellProfiler/tutorials/tree/master/Translocation

We also have video tutorials available that show how to use CellProfiler and CellProfiler Analyst to complete the Translocation tutorial:
CellProfiler workshop: https://www.youtube.com/watch?v=eriZdORpFxs&t=1s
CellProfiler Analyst workshop: https://www.youtube.com/watch?v=4aKRKrmzf60

Note that you can skip directly to the CellProfiler Analyst workshop if you prefer, but I recommend completing both workflows. In doing so, you’ll get a better idea of where the data that you analyze with CellProfiler Analyst comes from.

Happy analyzing,

Hi, thanks for your answer. I have watched the Translocation tutorial and learned a lot from it. But still, it’s a little hard to know how to use the program for my purpose. here I describe my project and also attach a picture of my cells then you can get a better idea of what is important for me to be able to do with those programs. Here I attach a picture of my cells. You see in the middle of the picture some long and elongated cells and I first want to use cell profiles for the images to be analyzed and segmented as you said and cell profiles can distinguish between the nuclei which are colored in blue and the actin filaments which are colored in red. Then I want to train the cell profiler analyst program to look for the elongated cells and quantify them in both treated cells and untreated cells so that I get an idea if the actual number of cells that are elongated is more in the treated cells than in the untreated cells (because I have seen such long cells in untreated cells too, but much less than I have seen in treated cells) then I can conclude that my substance has affected the morphology of the cells and that the appearance of the cells has changed after treatment with the particular substance. I need to first use cell profiler to create a property file and then use that property file in cell profiles analyst to learn and train the program to look for the cells I am interested in. And it is also important for me to know how to create the property file correctly. Thanks for your help in advance.6 M.tif (4.1 MB)

Thanks @Navid. Can you share your pipelines that you’ve created so far and explain where you’re stuck? That will help us tailor our problems to your solution.

You’ll also want to be sure to also watch the CellProfiler Analyst workshop, which will answer some of your questions: https://www.youtube.com/watch?v=4aKRKrmzf60

In general, your workflow is sound:

  • load images in CellProfiler
  • separate color images to grayscale using the ColorToGray module
  • identify nuclei using IdentifyPrimaryObjects
  • identify cells using IdentifySecondaryObjects with nuclei as seeds
  • make measurements on your objects using modules in the Measure category
  • then use the ExportToDatabase module to export an SQLite database and a CellProfiler analyst properties file
  • then you can use CellProfiler Analyst to create a classifier for your elongated vs round cells

I have now managed to convert the image from gray to color and have so far created identifyprimaryobject and identifysecondaryobjects and analyzed my image that sent you before. Has made some settings on the identifyprimaryobjects and identifysecondaryobjects modules. Here I send a picture of the color conversion from color to gray where you can see what the original picture looks like used by cellprofiler to analyze (same picture as I sent you before) and I have attached the result pictures for both modules and settings for both modules. As you can see in the pictures, it is not optimal, the program can not distinguish cell bodies in the right way. How do you solve this problem?