Using Fiji/ImageJ alongside CellProfiler to form Pipelines for Bin Analysis

Assistance required regarding forming pipeline please?

Hi @aiyshaelhaschemi, welcome to the forum! Congrats on undertaking these image analysis tasks. They are an important part of any research project and in my opinion, the most interesting!

With what you’ve described, I could imagine building a CellProfiler pipeline to:

  • Import your images; you will likely be able to import your images directly without using Fiji and then split the image into channels
  • Identify neurons, astrocytes, and other cellular entities as individual objects (one object type for each cellular entity of interest)
  • Making measurements in CellProfiler using our many measurement modules
  • Exporting these measurements to the software of your choice for further analysis

To get started using CellProfiler to analyze your images, we recommend watching this CellProfiler introductory workshop, which is available on the Center for Open Bioimage Analysis YouTube Channel. You can download the corresponding written tutorial on Translocation from the CellProfiler Github page. Once you get started building a pipeline to analyze your images, if you have questions, please do reach back out on the forum.

Good luck and great work getting the data to analyze!