python-bioformats
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CellProfiler
Read and write life sciences file formats
Hey everyone, first of all thanks for this amazing library, and all of the efforts of bridging the two ecosystems! I noticed that boto3 is listed as a dependency with...
Hi everyone! First of all: Great and very much appreciated bioformats wrapper! I encountered the following issue: My aim is to filter my images based on the channel. The images...
The `bioformats` java package was recently updated to properly handle certain `.dm4` files. My understanding is that this python wrapper package (specifically the `.jar` file) also needs to be updated...
I am trying to analyze a .ch5 ([CellH5](https://github.com/CellH5/cellh5)) file in python. This file opens fine in ImageJ with the Bio Formats plugin, but python-bioformats throws an error when calling `bioformats.ImageReader(file.ch5)`....
Fixes #129, Fixes CellProfiler/CellProfiler#3411 This PR addresses a long-standing issue with python-bioformats reading file metadata incorrectly, particularly when inspecting OME-TIF files. Within CellProfiler this manifested as the Metadata module "seeing"...
I'm getting a huge number of DEBUG and INFO level messages from bioformats when trying to read an image. Is there a way to suppress these? I wasn't able to...
On the https://pythonhosted.org/python-bioformats/, the provided link for the [OME-XML schema documentation](http://git.openmicroscopy.org/src/develop/components/specification/Documentation/Generated/OME-2011-06/ome.html) is outdated. The correct link is the following: (https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html).
I am using python-bioformats to read TIFF file. I get following this everytime. ``` 09:04:19.664 [Thread-0] DEBUG loci.common.NIOByteBufferProvider - Using mapped byte buffer? false 09:04:19.675 [Thread-0] DEBUG loci.formats.ClassList - Could...
I tried this in two environments, first with python3.9 and czifile installed, and then again in a fresh environment with python3.6. Same error. `conda install -c bioconda python-bioformats` returns ```...
I am using `python-bioformats` to extract metadata from the `Tif` file. I found a method called `getMetadata` which returns some Java object (as it says). This returned object has only...