OMETIFF.jl
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tlnagy
I/O operations for OME-TIFF files in Julia
Hi, My images was acquired by a Zeiss confocal microscope and saved images as ome.tiff. When I tried to load the file in julia, I got this error: ```jl julia>...
I need to thoroughly diagnose this, but I have multiple MicroManager images that have broken embedded JSON comments that cause the loading to come to a screeching halt at https://github.com/tlnagy/OMETIFF.jl/blob/7134699511ba12864a3b1a3b74331f40636e8f1c/src/files.jl#L200...
Saving OMETIFF is supposed as: 1. extract metadata from inside OMETIFF container, feed to omexml generator 2. reinterpret data to 2D into a TiffImage container, feed omexl to first ifd's...
Would be nice to add some nice Literate.jl example [like what I've done for TiffImages.jl](https://tamasnagy.com/TiffImages.jl/stable/examples/reading/)
I have .ome.tif files exported from lavision biotec's imspectorpro. ``` using FileIO tf = load("pathto.ome.tif") ``` Top part of stack-trace ``` Fatal error: ERROR: KeyError: key "Type" not found Stacktrace:...
For smart microscopy purposes, it would be very nice to be able to stream an OME-TIFF file as it is being written such that the loaded Julia struct gets updated...
Something to explore is whether the default structure of the underlying data (striped or not) should be encoded in the type of the out-of-memory object?
While #51 added support for read-only disk arrays, it would be nice to also be able to write data in a similar memory-efficient way. This will likely take some coordination...
This is a reversal on #10. I might follow ImageJ's convention and attempt to include position as just another axis if there are no conflicts in axis sizes, but return...