Open Microscopy Environment

Any suggestions for working with collections of hyperspectral images?

From what I can tell, it looks like I have 2 options:

1) Upload the hyperspectral TIFF stacks, and treat each spectral slice as a different z- or t-section.

2) Use MATLAB (or other tools) to render false-color RGB images from the original TIFF stacks (by projecting each pixel onto a set of spectra), and upload the results to OMERO.

What I would really like is to have OMERO generate the false-color image on the fly when previewing. Is it possible to do this?

Thank you!
-Jesse

Hi,

I'm afraid it's not currently possible to render a single-channel image as "false-color" in OMERO, although we are looking to support this in the future.

So, if you need to view false color images in OMERO, your only option would be to use another tool to render to RGB images then import those, although you won't then be able to change the rendering settings of intensity -> false color in OMERO.

If you want to import hyperspectral TIFF stacks into OMERO, it may make most sense for these to be multiple Channels, instead of Z / T sections.
What do you get if you import your data into OMERO? (z-stack, t-stack, separate images?). If you get separate images, there is a 'Combine_Images' script to create a single stack image from these. Is the lack of false-color rendering a blocker for this option anyway?

I'll note your request for false-color rendering (lookup tables), but if there's anything else we can help you with, let us know.

Regards,

Will.