Permissable File Extensions?

cellprofiler

#1

Greetings All,

What are the permissible types of image files that Cellprofiler can use? I have a Biorad Versarray Colony Picker robot that only saves images as .bmp files. The only file type I find mentioned in the help pages is .tif files, which are talked about in the LoadImages and LoadSingleImage Modules. Will .bmp image files work just the same, or not? I appreciate any help.

Thanks,

William C Colley


#2

Hi William,

If you are using the developers version of CellProfiler, you can type “CPimread” in the terminal and it will return a list of readable image formats. Here is its output:

CPimread

ans =

Columns 1 through 11
’bmp’ ‘cur’ ‘fts’ ‘fits’ ‘gif’ ‘hdf’ ‘ico’ ‘jpg’ ‘jpeg’ ‘pbm’ ‘pcx’

Columns 12 through 22
’pgm’ ‘png’ ‘pnm’ ‘ppm’ ‘ras’ ‘tif’ ‘tiff’ ‘xwd’ ‘dib’ ‘mat’ ‘fig’

Column 23
’zvi’

So bmp files should not be a problem!

Mike


#3

Greetings All,

Thank you for the information Mike. I have managed to open bitmap files with Cell Profiler. Now I just have to define a set of images to use as a template to develop my applications.

At this time I am not using the developers version, but I am having to use both PC and Mac versions as the images are generated on a PC but the client only uses Mac. Assuming that the applications I develop are to be implemented for routine use I will have potentially many hundereds to several thousands of images to analyze per experiment, so I would have to move the applications to the CP cluster version instead of a desktop version.

I am sure I will have more questions, and all sugestions are appreciated.

William C Colley


#4

Hi William,

There have already been some posts on using the cluster version of CellProfiler which you can read through, but if you need any help please ask.

Regards,
Mike


#5

p.s. be sure to check out the Example Yeast Colonies on the cellprofiler.org/examples.htm website because that should provide a good starting point for you.
Cheers,
Anne


#6

I am trying to load zvi files into cellprofiler and I am getting an error message. Is it even possible to load zvi files?


#7

Hello,
I’m not sure why your message is in this particular thread, but in any event, we have been able to adapt CellProfiler to read some ZVI files. If you have downloaded the latest version of CellProfiler and are still unable to open your ZVI images, please let us know the exact error message and post (on a publicly available website) one of the files you are trying to open and we will see what we can do!
Cheers,
Anne