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How can I split a multiposition ".lsm" file into multiple single position ".lsm" files?

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I am working on Imaris and big files are not simple to handle with this software. After a certain position it start to mess up with the channels and so on.

I tried a home made macro from our Bio-optic dep but it does not work for large files (30 go) with 150 positions.

Does anyone know any thing about how to split this files?

On Zen, ImageJ/FIJI or something like that?
asked Oct 20, 2014 in Image analysis by Benoit (120 points)

1 Answer

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are the positions saved in an image stack?

If so, you could use "Fiji" to separate them into single files.

The manual way would be:

Open the stack with Fiji

Goto "Image" > "Stacks" > "Stack to Images"

Save each image.
(Saving as .lsm will not be easy (impossible with fiji?). You could use the OME-TIFF format to save your images with meta data. If you really need the LSM format, there would be the possiblity to write a utility as this format is just a modification of the TIFF format but this would be a lot of work.

Of course it is possible to have the steps done automatically with a little script. Let me know, if you need help to create such a script.



answered Oct 20, 2014 by cri (420 points)
edited Oct 20, 2014 by cri
Actually my single position are not save as stack but as frames.

For each single position or frames on imageJ, I have like 80 z stacks and 4 channels.

Is there any way to save directly each frame into a single files on ImageJ?

For the output files, I would need a type that could be open by imaris.
ok, its a hyperstack in this case.
Go to "Image" > "Hyperstacks" > "Reduce Dimensionality"
You can select what you want to have in the resulting image.

Imaris should be able to work with TIFF files. In this case you probably will lose the meta data. I think it won't be stored in TIFF images. (Maybe you don't care anyway).

Try, if you can extract the information you need, manually. We can think of automatizing this tasks afterwards.