Is CPcharm the best program to categorise the morphologies of mitotic chromosomes?

Usage & Issues
#1

I will be really grateful if you could recommend which program is most suitable for our application.

I thought about “CPcharm" would be best for our purpose below but I am open to any suggestion.

Also I am wondering if I need to download earlier version of Cellprofiler (v2) to use “CPChram”.

I am also worried that having both Cell profiler (V4) and V2 on my computer would cause any problem.

Our aim is to classify chromosome images of wild type and various mutant cells (vertebrate cell line) synchronously entering mitosis from G2 phase.

Basically we have set of DAPI stained image sets at G2, 2.5 min from G2, 5 min from G2, 7.5 min from G2, 10min, 15 min, 30 min.

In general,

G2: interphase

5 min: most cells are prophase

7.5 min: mix of prophase and very early pro metaphase

10 min: early pro metaphase

15 min: mid pro metaphase

30 min: late promeatpahse, metaphase

But we want to quantify the progression of individual data set and compare wild type and mutant cells at individual data point.

This is not high-throurghput images. Each data set would contain max 50 images.

We do not really need to measure the length/width of chromosomes. We just want to classify the morphologies.

Thanks you very much for your advice in advance.

Best regards,

Kumiko

#2

Hi @kumiko,

There are many bioimage analysis software programs that could be used for the problem you describe. One option is to use CellProfiler 4 to identify and measure your cells. You can then use CellProfiler Analyst to train a machine learning classifier to distinguish between images of cells in different stages of the cell cycle.

If you’re new to CellProfiler, 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. Note that the translocation tutorial has a similar workflow to what I’ve described above, with a combination of CellProfiler and CellProfiler Analyst. A CellProfiler Analyst tutorial is also available on the COBA YouTube channel. Once you get started building a pipeline to analyze your images, if you have questions, please do reach back out on the forum!

Best,
Pearl