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Hi,
I frequently work with confocal microscopy images stored in the LSM
file format, and as Zeiss's LSM software only works on Windows, I
have been attempting to use ImageJ on my MacBook (OS X 10.4.10, 2 GB
RAM, ImageJ 1.39c). I am in the process of writing a batch macro to
do the following:
1) Step through all the folders/subfolders inside a given directory
and process each .lsm file encountered.
2) For each .lsm file, perform an RGB merge (merge red and green
channels).
3) For each single image, export to jpg.
4) For each stack encountered, perform a 3D projection (x-axis,
brightest point, with interpolation). Save as a QuickTime movie.
I have not gotten the macro to completely work successfully. So, I
have two questions:
a) When trying to do an RGB merge, I often run into the error "No
image(s) open" even though ImageJ has just opened an image. Is there
a required "sleep" time before I should attempt to perform the merge?
b) I can easily do a 3D projection using Zeiss's own LSM software on
Windows computers with low RAM (512 MB). However, ImageJ typically
requires substantially more memory, and with the interpolation option
enabled, I am frequently running out of RAM (I have allocated 1500 MB
and I always hit the limit). Am I correct in concluding that there is
no way around this problem?
Thanks for any help you can provide.
Peter Yang
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