Sending data from Imaris to Matlab.

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IronFish
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Joined: Thu Dec 15, 2011 1:54 pm UTC

Sending data from Imaris to Matlab.

Postby IronFish » Thu Dec 15, 2011 1:57 pm UTC

Hi folks !

I've imaged some cells ; the data is in the form of .lsm files.
I have Imaris at the uni.
How can I export the data to something readable by Matlab?

Thanks
:)

rflrob
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Re: Sending data from Imaris to Matlab.

Postby rflrob » Thu Dec 15, 2011 6:55 pm UTC

I'm a big fan of using ImageJ to convert files to formats usable by other programs (.tif works in Matlab; I'd be wary of this format, though, if a) that your images are stacks, and b) there's a chance you'll ever switch to Python for your data analysis. In that case, I prefer FITS files). I don't know if it can do .lsm files natively, but it appears there's a library, BioFormats, that can read 'em and is linked to from the ImageJ site, so it's a good bet there's a plugin somewhere.

Once you have ImageJ, there's a Batch Convert feature under Process > Batch > Convert.
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iop
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Re: Sending data from Imaris to Matlab.

Postby iop » Sat Dec 17, 2011 5:52 pm UTC

I am wary of converting to .tif, since you lose the meta-information about your image.

To import images into Matlab, I like using the [http://www.loci.wisc.edu/bio-formats/downloads]bioformats[/url] reader (which is what ImageJ uses as well). I have written a Matlab wrapper for it; PM me if you want it.

If your Imaris license includes the XT module, you can also use Matlab to connect to Imaris in order to use their loaders to grab the images (and to send back e.g. segmentation results).

IronFish
Posts: 9
Joined: Thu Dec 15, 2011 1:54 pm UTC

Re: Sending data from Imaris to Matlab.

Postby IronFish » Wed Dec 21, 2011 2:24 pm UTC

Thanks a lot, folks!


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