How do I convert pixels into µm in cellprofiler program?

[Nikhil_rao]

I have been calculating area in pixels but that is not it should be represented while publishing an article. Can anyone help me with how I can use the program to convert from pixels to µm. Thank you.

/Nikhil

[lakshmi (Lakshmi Balasubramanian)]

Hi Nikhil,

Generally, Cellprofiler gives in pixels. The pixel to micrometer conversion you have to do it. Unfortunately, program doesn’t do. Useful old links,

Setting pixel to micron scale for correct area

Dear All, I have been using Cell Profiler for the last few days and have made a pipeline that works surprisingly well. My concern is that the area may not be accurate. Previously, in ImageJ we would “set scale” based on the objective of the microscope. This allows for accurate estimation of area. I have been using images captured with a 10X objective to practice with. The size that it is generating seems like it may be right but how does the software determine how long (in microns) the pix…

CellProfiler 2.0 FAQ

This thread lists some of more commonly asked questions we come across in the forum. Feel free to add requests to this thread if you think of a general question that would be broadly applicable to many users!

Regards,
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com

[bcimini (Beth Cimini)]

If you know your own pixel-to-micrometer conversion factor, you can multiply it directly times any 1D measurements (radius, etc) and multiply it squared times any 2D measurements (area, etc)- you can either do this yourself after-the-fact, or in the CalculateMath module.

[Nikhil_rao]

Thank you very much bcimini.