Micro-Magellan file format compatible with OMERO?

Hi all,

I am planning to run a new spinning disk confocal microscope on Micro-manager and use the Micro-Magellan plugin for imaging large, fluorescently stained tissue sections. Since my lab uses OMERO for all data storage and visualisation, I would like to know what data format Micro-Magellan uses and whether is is compatible with OMERO. All its information page seems to say is that it is a multiresolution file format, but I can’t find any specifics.

Hi @kkwakwa, Im unaware if this is a unique format but based on https://micro-manager.org/wiki/MicroMagellan#Saving it seems to at least be compatible with Big Data Viewer and has an option to convert to Imaris files. Support for the BDV format has been added to Bio-Formats and should be available from OMERO 5.5.0 and up and Imaris files should also be supported. That being said I have never actually seen or tested a dataset from Micro-Magellan so I cant say for sure if it is fully supported. If you have any sample files from Micro-Magellan I can happily check those for you.

Hi @dgault, The microscope I will be using isn’t ready yet, so at the moment I don’t have any raw data yet. As soon as i do, I am more than happy to send you some. I’m hoping it is stored in BDV format, but heir documentation also mentions that you have to copy in an extra jar file in order for BigDataViewer to recognize the file format, meaning it may be something slightly different.

I guess I could look through their source code and see if that gives me any ideas.