Morphology Analysis of a batch of images at once

cellprofiler
batch-processing
morphology
cellsize
pipeline
brightfield

#1

I have a big set of images (bright-field), and I need to get data on cell morphology for each (size, roundness, aspect ratio, etc.). I am new to cellprofiler, and I have tried the “Load an example pipeline” option…the result from this analysis is exactly what I am looking for: an excel sheet with all the morphological information about the cell.

My questions are:

  1. Is it possible to use cellprofiler for unstained (bright-field) images?
  2. How do I run the same pipeline as the one in the “example pipeline” but on my own set of images?

Would appreciate an answer in simple terms as I am a beginner in image analysis.


#2

Hi Baryam,

I have made changes in the pipeline so that it can be used for brightfield images. However you need to tune parameters for segmentation according to your experimental needs.

pipeline.cppipe (16.8 KB)

Regards
Hamdah