[ome-users] Exception thrown when importing Micro Manager dataset with Bioformats

[Mark Carroll]

Dear Dave,

> We’re using Micro Manager 2.0-beta3. I’ve uploaded a sample metadata
> file – I can see that the formatting is slightly different and this is
> obviously the cause of the problem.

As at
https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/micro-manager.html
I am afraid that Bio-Formats supports only up to Micro-Manager v1.4.22.
As I understand it https://github.com/micro-manager/micro-manager is
v2.0beta and https://github.com/nicost/micro-manager/tree/ViewerPlusCV
is v2.0gamma and the two are works in progress that are not
API-compatible. The Micro-Manager community may wish to correct me on
this. The short story is that we are not aware of a v2.0 format
specification document and v2.0 support is not in our current plans.

In recent times new reader code has tended to come from other sources
such as commercial collaborations with Glencoe Software. Within the core
OME team our open-source side has been focused on other requested work
such as developing better support in OME-TIFF for pixels pyramids. If
Bio-Formats reader support is needed in the near term for the new
Micro-Manager v2.0-xxx formats then as an open community project we are
certainly glad to help others along in that work and to review their
code for possible inclusion into mainline Bio-Formats. In the meantime
thank you for your data submission and related clues as those are always
helpful for getting and keeping any eventual implementation correct.

-- Mark

The University of Dundee is a registered Scottish Charity, No: SC015096