Open Microscopy Environment

Hi all,
I am having trouble importing the Leica Z16 metadata from Z stacks (or even single images) through Fiji Bio-Formats. LAS produces four different files of metadata, three of which (.anx, .eax and .sbx) can be drag easilly by the scrolling tool. But in the end nothing happens, the scale values (pixel size) are not detected by the plugin; so you have to incorporate all the data manually. Should be easy, as the data are there (especially in the .anx file), so I wonder if there is anything wrong in my procedure or simply LAS metadata from Z16 are not supported.
Thank you.
Joaquin

Hi Joaquin,

Unfortunately this particular format is not yet supported. We certainly have a growing backlog of many tens of new file formats, the Leica Stereo Microscope is amongst these - https://trello.com/c/rLrDJkJj/6-leica-stereo-microscope

Developing and testing new file format readers is significantly more costly than maintaining existing ones. Our priorities are necessarily our current academic deliverables (http://www.bbsrc.ac.uk/documents/2016-t ... d-grants/; https://wellcome.ac.uk/what-we-do/direc ... ple-funded), which do fund cross-platform resources for writing OME-TIFF (https://www.openmicroscopy.org/ome-files/) and support for several binary formats (BDV, etc.). While we certainly want to support as many formats as possible, the seemingly eternal development of new formats is hard to prioritise, given other pressing needs.

On the other hand, we will review any external contribution with new reader additions and consider their inclusion in a minor release of Bio-Formats. We have had several additions of this kind over the past few years and we always welcome independent community contributions to Bio-Formats as well (https://www.openmicroscopy.org/contributors/).

We are dedicated to maintaining Bio-Formats, but also, in the best spirit of open source development, sourcing contributions from the community for new formats.

David Gault

Hi David,
thank you very much for your inmediate reply and detailed information. I perfectly understand the limitations and will explore any possibility to contribute actively.
All the best.
Joaquin