LSM files

Hello everyone,

I am new to working with CellProfiler. I am using WormToolbox to analyze brightfield, GFP, and mCherry images. Right now I have to acquire my images using a Zeiss D510 LSC running Zen. However, that means the images are one LSM file with all 3 channels in it. I am using ImageJ to split the color channels and save them as separate tiff files for analysis by CellProfiler. Is there any way CellProfiler can do this automatically? I am going to have hundreds of images eventually, so doing the conversion manually will become onerous.

Thank you for a fun and exciting program!



Hi Rachel,

There are a couple of ways we can proceed on this:

  • Do you have the option of saving the files as ZVI (which I believe is Zeiss-supported)? If so, you can adjust the file type in LoadImages to “tif,tiff,flex,zvi” and some new settings will appear which will allow you to specify the individual channels from each file and name them. This is the most straightforward solution.

  • Since CellProfiler uses Bio-Formats to read images, LSM is supported, but the .lsm extension is not currently recognized by CellProfiler. We could enable this extension, and then point you to newest (but unreleased) build. This is fairly simple to do, but by using the newest build, you would be incorporating some of our newest development work and you would essentially be using an untested prototype.


Thanks for the advice. I will try using ZVI, if it doesn’t work, I wouldn’t mind trying something untested. It would be an adventure :smiley: