Convert LSM confocal images to other formats

cellprofiler

#1

Dear Team,

Here is a very typical problem I’m facing and probably others will face.
I had designed a complete pipeline for images from High-content Imaging.

Recently, with new developments, we are using Confocal Imaging and so, the images are in ‘lsm’ format with a database structure.

Is there any way, by which I can read these LSM images in CellProfiler and can convert them into bmp/tiff formats for each of the channel.
I’m using three channels for the experiments.

Your guidance will be great in solving this issue.
Thanks
Mridul KK


#2

Hi Mridul,

Thanks for suggesting this, we’ll look into it; currently Matlab’s imread does not support lsm file formats, but users have created tiffread, which can read lsm files:
mathworks.com/matlabcentral/ … tType=file
If you are using the developer’s version, you can implement this function instead of imread where it is called in CPimread (the CellProfiler subfunction which reads image data).

Hope that helps!

~kate


#3

Thanks Kate.
I’ll look into it.
Mridul KK