Forming a Pipeline using CellProfiler for Quantitative Analysis


I’m trying to analyse TIFF files by attempting to create a pipeline using CellProfiler. For easy viewing purposes, I have uploaded JPEG examples below:

(Where Image 1: Astrocytes visible due to GFAP antibody,
Image 2: Neuronal cells visible due to NeuN-biotin Antibody,
Image 3: DNA nuclei visible due to DAPI,
Image 4: [Composite image])

However, I have been unsuccessful in creating an appropriate pipeline to identify each separate entity (astrocyte/neuronal cell/DNA nuclei) and am then further wanting to undertake quantitative analysis, i.e. how many astrocytes, neuronal cells, DNA nuclei present, so I can export to Excel and carry out statistical analysis (bin analysis - most likely).

Is anyone able to help please? I’ve attempted to watch so many tutorials and use examples but nothing seems to work.

Thank you :slight_smile:

Hi @aiyshaelhaschemi,

We’ll be happy to help! The best way for us to help you learn to use the program is if you start building a pipeline (based on our CellProfiler workshop on the Center for Open Bioimage Analysis YouTube channel CellProfiler Workshop - YouTube) and then reach out to us with example images and your initial pipeline to explain where you’re getting stuck.

A general strategy might be to:

  • identify nuclei using IdentifyPrimaryObjects
  • then identify neuronal cells using IdentifySecondaryObjects with the nuclei as seeds
  • identify astrocytes using IdentifySecondaryObjects with nuclei as seeds

You can also download examples to modify from our website. Examples | CellProfiler

Good luck!

1 Like

Hello, thank you for your message.
I attempted that but my resulting images were unsuccessful. I will try again following your advice and return to the forum if I still need aid.
Thank you ever so much.

We’re happy to take a look at pipelines that are a work in progress! You can always share the pipeline file and example images and let us know where you’re stuck.

Good luck!