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CellProfiler / python-bioformats

Read and write life sciences file formats
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Possible strategies to include new features of BioFormats 5.3.1 #76

Open sebi06 opened 7 years ago

sebi06 commented 7 years ago

Hi,

you probably know that the new BioFormats 5.3.1 has some features that allow switching on/off reading tile images as a whole or as single series (like it was in the past). Additionally it can read pyramid levels from tile images. Both things are very useful features, but so far the cannot be used from the wonderful python-bioformats library, right?

There are already some suggestions on how this might work out but this still needs to be dicussed in detail. See also: https://github.com/openmicroscopy/bioformats/issues/2697

I would be very interested in your thoughts about this and on your possible roadmap to integrate this new things.

Sebi

sebi06 commented 7 years ago

HI guys, are there any news on this issue? I would really appreciate some input here, since working with files containing multi-resolution image series can be really tricky.

Sebi

mcquin commented 7 years ago

Hey @sebi06 -- very sorry about the radio silence!

I'm working on updating the bundled version of loci_tools to 5.5.3 (see: #83). Once that's in, we'll be able to work on making the ImageReader/ImageWrapper classes more flexible. The suggestions made here are both good and (hopefully) aren't difficult to implement.

sebi06 commented 7 years ago

Hi, that are good news. Let me know if I can help. Maybe with test data directly from Zeiss, since I am in charge of the CZI file format there?

Am 18.08.2017 3:55 nachm. schrieb "Claire McQuin" <notifications@github.com

:

Hey @sebi06 https://github.com/sebi06 -- very sorry about the radio silence!

I'm working on updating the bundled version of loci_tools to 5.5.3 (see: #83 https://github.com/CellProfiler/python-bioformats/pull/83). Once that's in, we'll be able to work on making the ImageReader/ImageWrapper classes more flexible. The suggestions made here https://github.com/openmicroscopy/bioformats/issues/2697#issuecomment-267559233 are both good and (hopefully) aren't difficult to implement.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/CellProfiler/python-bioformats/issues/76#issuecomment-323360270, or mute the thread https://github.com/notifications/unsubscribe-auth/ADp9obI2E0NRU2lFOtAEih_e4gKnfX9aks5sZZe5gaJpZM4LUuN2 .

yfukai commented 3 years ago

Hi there, a kind of late for the party for years, but please allow me to advertise my code related to this issue. (I hope it's appropriate but otherwise please let me know.) I wrote a piece of code to read a tiled CZI image (without automatic stitching) through python-bioformats, and packaged it as a thin wrapper https://github.com/yfukai/pycziutils (quite preliminary but tested and usable, I hope.). In case this issue is still not solved, and if it would be useful to integrate a part of my code into the python-bioformats itself, please let me know as I might be able to do some work. Cheers!