ome-tiff multidimensional tiled image examples
Posted: Thu Jan 07, 2016 5:04 pmHello:
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
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