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Matt J. Renshaw

we're currently trialing out OMERO but are having issues with the larger datasets that are generated from our Micromanager 2.0 (beta) live cell imaging systems: multiple positions, multi-C, z-stack timelapse experiments, so we're talking >500GB of data. Importing the data into OMERO works well (obviously as it's Bioformats...), but subsequently reviewing the data is very sluggish. With the large size these datasets need to be reviewed as virtual stacks and although this works very well when using Micromanager, when going through bioformats (OMERO and FIJI) it's painfully slow.

Glencoe have said it is due to duplication of the metadata in the ome.tiffs produced by Micromanager and we're pushing for a workaround. However, has anyone noticed a difference in performance with the different options for saving files (i.e. single tiff files, tiff stack, separate tiff stack for each XY)? I currently set the systems to save each XY position as an individual tiff stack as in most cases this allows the files to easily be opened in FIJI simply by dragging and dropping. I'm wondering if it would be better to not separate the XY positions?

Many thanks,

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