Open Microscopy Environment

Hi Omero admins,

I asked for some functionality to be added in for a less prevalent file format to be added in to loci_tools and Melissa Linkert was gracious to add this in.

Here is the original post,
viewtopic.php?f=13&t=2573

here is the Trac#
http://trac.openmicroscopy.org.uk/ome/ticket/9930

and finally here is the GitHub discussion,
https://github.com/openmicroscopy/bioformats/pull/317

My question is on how to add this functionality to Omero so that images imported work successfully. Is there a corresponding loci_tools.jar I could replace? (Though I couldn't find one)

-J

Hi Joshua
We do not have a mechanism in place to automatically update the jar bundle with the application (i.e. mechanism in place in Fiji for example)
If you are using the client on mac, you could replace the jars (bioformats.jar+ associated if modified e.g. loci-common.jar) by right-clicking on the application
Show Packages contents>Contents> Resources> Java

Are you using directly the command or drop box to import the files?

Jmarie

I don't mind how I import the files as long as I could use the extra functionality. I think this portion is done on the omero server itself ... or I could be wrong. If using insight on a mac, what files would I swap out? I have a custom compiled loci_tools.jar that works its magic for me when using the command line.

-J

Forgive me for being naive but I just want to confirm that Omero is similar to Fiji/ImageJ in that it uses BioFormats libraries to translate the images from (proprietary?) native to OME-TIFF?

J

Yes, OMERO uses bio-formats to read the files
jmarie

OK, so on the server is it possible for me to change out some files to enable the functionality that the newer bioformats has?

J

Yes you can modify directly the bf jars you want to update:
Note that we do not use the loci_tools.jar but bio-formats.jar, jai_imageio, loci-common etc.

Jmarie