python-bioformats
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CellProfiler
Read and write life sciences file formats
There was a [previous issue](https://github.com/CellProfiler/python-bioformats/issues/121) on this but it was closed without answer. I'm trying to instantiate the bioformats.OMETiffWriter class but it crashes on instantiation: ``` writer = bf.OMETiffWriter() AttributeError:...
Optionally load the `SlideBook6Reader.jar` if the file is present. This adds (native) support for loading 3i's `.sld` files. The JAR can be fetched from the corresponding [SlideBook Fiji update site][1]...
This PR is adding unit tests for the functions added in 3e58906d71466e9396b6b6b03c68f55767459a82 ff.
Use the "setuptools_scm" package to automatically generate the version of the package as well as the corresponding variable available in the code. This fixes issue #86 while still leaving open...
The fix merged in #86 being https://github.com/imcf/python-bioformats/blob/08161368eebea17578d03e7c8fe52211d4f454ce/setup.py#L42-L45 got silently removed (again) in 2d487239b3a8d531e69342cec89ca2395cd0e56a, resulting in a call to ``` import bioformats print(bioformats.__version__) ``` returning `’0.0.0’` (again).
I'm currently using python-bioformats to extract OME XML from confocal data using data that I'm pulling from AWS S3 using [s3-streaming](https://pypi.org/project/s3-streaming/). In order to do this, I have to first...
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...
In an image from the [forum](https://forum.image.sc/t/metadata-reading-problem/51191/3?u=bcimini) (image attached here as well). Fails to open in CellProfiler with the error below, metadata etc posted underneath. [Spat-1-1.oir.zip](https://github.com/CellProfiler/python-bioformats/files/6287390/Spat-1-1.oir.zip) ``` [Fatal Error] :1:35: Character...
It would be great if there were installation instructions. For example, the right version of java has to be installed first, otherwise, just 'pip install python-bioformats' will fail. I'm trying...
Hi. So I'm new here, will try to post as much info as I can. I have installed javabridge, using pip intstall python-javabridge. it works, and I know that because...
