Open Microscopy Environment

Hello:

We are working on instrumentation and software to collect 4D data (2D + channels + z stack) in a tiled format, and we'd like to save the data collected directly into OME Tiff. We're working in Python and attempting to utilize Bioformats by wrapping the Java, and/or using Python javabridge. There are some caveats to this approach, but we are trying to work through them.

We're familiar with the guidance at:
https://www.openmicroscopy.org/site/sup ... mages.html

One thing that would really help is access to some example ome-tiff image data that incorporates channels, zstacks and tiles to ensure we are doing things correctly. So far we haven't been able to find such example data in open repositories--are we missing anything? We're considering trying to gather xyzc+tile data from a Zeiss Axioscan and then export to ome-tiff but we aren't sure if this will produce correct output.

Thanks for any help you can provide--we really appreciate it.

Sincerely,
Karl

Hi Karl,

kegarsha wrote:We are working on instrumentation and software to collect 4D data (2D + channels + z stack) in a tiled format, and we'd like to save the data collected directly into OME Tiff. We're working in Python and attempting to utilize Bioformats by wrapping the Java, and/or using Python javabridge. There are some caveats to this approach, but we are trying to work through them.

Interested to hear any feedback on this approach, perhaps separately when you're ready.

We're familiar with the guidance at: https://www.openmicroscopy.org/site/sup ... mages.html

One thing that would really help is access to some example ome-tiff image data that incorporates channels, zstacks and tiles to ensure we are doing things correctly. So far we haven't been able to find such example data in open repositories--are we missing anything? We're considering trying to gather xyzc+tile data from a Zeiss Axioscan and then export to ome-tiff but we aren't sure if this will produce correct output.

As mentioned under viewtopic.php?f=6&t=7983, sorry for the slow response. Several of us are on the road and this is unfortunately something we'd prefer to have a better answer for.

You might start off by taking a look over the ome-devel thread, "File format for large data sets stored at multiple resolutions", from May last year. Though we certainly owe the community a report, the status is still largely that we've held off on defining a tiled or pyramidal file format, both to see what happens with the existing formats like DICOMs Supplement 145, BDV, etc. as well as to gauge community demand. Your post like a recent mail on the openslide-users list certainly points to interest.

In the mean time, you still need something you can begin evaluating. Of our existing examples, does http://downloads.openmicroscopy.org/images/OME-XML/2015-01/spim.ome.xml, which stores tiles as individual images, look like a place to start?

All the best,
~Josh.