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.
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?
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!