Micromanager and OMERO

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Micromanager and OMERO


This has been sent to both the OME user list and to the Micro-Manager list.

I have some general questions and comments about the ome-tiff files generated by Micro-Manager (MM), their metadata, and Bio-Formats/OMERO compatibility.

Question 1:
I recently finished implementing an OMERO.server with a OMERO.web interface, together with the OMERO.figure & OMERO.iviewer apps (good job BTW, users and PIs LOVE these!).
However, neither OMERO.viewer or OMERO.figure display correct time points on timelapse data we generate.
It seems like OMERO/Bio-Formats is not correctly reading (or utilizing) TimeIncrement & TimeIncrementUnit from Micro-Manager generated files, even though the deltaT value for each image is displayed correctly.
We are running both MM 1.4.23-nightly and 2.0-beta-nightly to control our microscope, depending on user preference.
I occasionally upgrade the nightlies, but the problems I describe are common for all versions tested.

How can I get correct TimeIncrement & TimeIncrementUnit values set for my existing Micromanager generated data in the OMERO.server/web environment?

Question 2:
During the setup of the MM configuration files I have been very systematic and thorough, so that all relevant data (filter bandpass, product numbers, objective NAs, etc...) is captured in the Micro-Manager metadata through informative device and property names.
As a facility manager it would be very helpful for me and my users to have easy access to this data through OMERO.

Is there some plugin/app/script that makes the Micro-Manager metadata accessible on the OMERO.server, or at least viewable from the web interface?
If not, I can try to implement one. I have spent some time reading through tif-tags and MM metadata for other projects, but there is no need to reinvent the wheel if there is something out there.


It has always annoyed me that MM ome-tiff files won't display a correct frame interval when drag&dropped into ImageJ/FIJI.
On the other hand, if images are instead opened through the Bio-Formats Importer, then they loose their LUTs (but gain the lost frame intervals).
The lost LUTs is also a (minor) issue when importing MM data to OMERO.server.
I suspect that this is because ImageJ has its own TIF-tag that stores imageJ-metadata, and that there is some inconsistencies in how MM writes the tif tags here.

Anyway, thanks for great softwares everyone, let's make them even better!

Dr. Jens Eriksson, manager
Sellin Imaging Platform
Dep. Medical Biohecmistry and Microbiology
Uppsala University

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