Cell size distribution


#1

Hi, i just begin to use the cellprofiler. The pictures i took for the cells are full moon eclipsed shaped(the edges are darker, the cell plasma and background is brighter). Which modules should i use to measure the size of the cells… Thanks…


#2

Hi,

I would suggest going to cellprofiler.org/examples.htm and have a look at the example pipelines. Based on your brief description, the fly and human tumor cells might be worth examining. The module MeasureObjectAreaShape would be the one that you would use to measure the size of your cells.

Generally, the workflow of any pipeline is (1) loading the images in, (2) identification of the objects of interest, (3) measurement of the features of interests from the identified objects, and (2) saving the output. As you examine the pipelines, keep this in mind when you start making modifications. And please remember that the example pipelines are examples only and may require some adjust for your images.

Hope this helps!
-Mark


#3

Thanks, Mark.
I also have a question about image requirements. Are there any restrictions on size and format of the images to be processed?


#4

We support most the typical formats (TIF, JPG, PNG, etc). Generally, we recommend that people use lossless formats like TIFs and PNGs.

There are no specific restrictions on image size, but most images we deal with are not much bigger than ~3MB in size, perhaps 2000 x 2000 pixels or less, depending on the format. If the images are too big, you will encounter out-of-memory errors after several cycles, in which case, you can follow the advice given in Help > General Help > MemoryAndSpeed.

Regards,
-Mark