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CellProfiler/python-bioformats
Failed install

Hi, I m running Python 3.13.4, with numpy version 2.3.0 on Windows 11. I got a very long error which I ll paste below, but I imagine this is just from using an unsupported version of python. Is there ...
  • bill-connelly
  • 1
  • Opened 
    on Jun 12
  • #176

CellProfiler/python-bioformats
Release plans

Is there a plan to release a new version with updated bioformats (8.1.1)?
  • amrosado
  • 1
  • Opened 
    on May 7
  • #175

CellProfiler/python-bioformats
Support for WSI pyramids?

I could not find any bindings for methods docummented here: https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/wsi.html Are WSIs supported at all by this wrapper? Is there a different way of ...
  • Aiosa
  • Opened 
    on May 5
  • #174

CellProfiler/python-bioformats
error: java.lang.ClassNotFoundException: loci.formats.in.URLReader

java.lang.ClassNotFoundException: loci.formats.in.URLReader
  • chengdonglin
  • Opened 
    on Mar 6
  • #173

CellProfiler/python-bioformats
python-bioformats support qptiff file?

python-bioformats support qptiff file?
  • chengdonglin
  • 1
  • Opened 
    on Mar 6
  • #172

CellProfiler/python-bioformats
How do I turn off debug output? When I read the image, it produces a lot of output

Does this information affect my reading speed? I m comparing the read speed of this library with openslide for the same whole slide image file. I think the text affects the results of the comparison. By ...
  • CDPDisk
  • 2
  • Opened 
    on Nov 28, 2024
  • #171

CellProfiler/python-bioformats
ModuleNotFoundError: No module named 'numpy' when installing python-bioformats

When I try to instal python-bioformats, I get this error. ModuleNotFoundError: No module named numpy Although I already did installed it. If I install python-bioformats without using --use-pep517 , I ...
  • d4nvjpl0ng4n
  • 1
  • Opened 
    on Aug 14, 2024
  • #169

CellProfiler/python-bioformats
Bug in opening Olympus *.vsi metadata for multi-dimensional (multiZ) files.

Hi, I am trying to open Olympus *.vsi file with : xml_str=bioformats.get_omexml_metadata(path) Reading a .vsi file with a single focus plane succeeds, but attempting the same with vsi files that contain ...
  • LyesSp
  • Opened 
    on Mar 12, 2024
  • #168

CellProfiler/python-bioformats
Can't get well plate information from OMEXML

I m not able to get plate or well information from the OMEXML object. I tried with a couple operetta format well plate images and an InCELL format image, both have this behavior. Here is a minimal example ...
  • JKelle
  • Opened 
    on Feb 19, 2024
  • #167

CellProfiler/python-bioformats
Upgrade bioformats_package.jar

Hi, bioformats_package.jar older than 6.13 uses snakeyaml 1.32 which has a security vulnerability CVE-2022-1471. bioformats_package.jar 6.13 and later use snakeyaml 2.0 which has the fix. So python-bioformats ...
  • Sravani-K
  • Opened 
    on Dec 28, 2023
  • #165
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