Problems opening a Nikon .nd2 file

[Clarion]

Thank you first of all for putting the pims module together!!

Unfortunately, I am running into problems opening Nikon .nd2 files.

Here is what I do:

mamba create --name imageprocessing python=3.10 -c conda-forge
mamba activate imageprocessing 
mamba install jupyterlab -c conda-forge 
mamba install python-javabridge -c conda-forge  
mamba install pims -c conda-forge   

When I run the following cell in a jupyter notebook, I get the error message below. And I can’t figure out what the problem is:

import pims
import javabridge
import bioformats

javabridge.start_vm(class_path=bioformats.JARS)

a = pims.open('/Users/c_osman/Documents/Python/Lab_scripts/Microscopy/510-150.nd2’)

Error:
/Users/c_osman/mambaforge/envs/imageprocessing/lib/python3.10/site-packages/pims/api.py:204: UserWarning: <class 'pims.bioformats.BioformatsReader'> errored: 'NoneType' object has no attribute 'isJVMStarted'
warn(message)

UnknownFormatError Traceback (most recent call last)
Cell In[1], line 7
3 import bioformats
5 javabridge.start_vm(class_path=bioformats.JARS)
----> 7 a = pims.open('/Users/c_osman/Documents/Python/Lab_scripts/Microscopy/510-150.nd2')

File ~/mambaforge/envs/imageprocessing/lib/python3.10/site-packages/pims/api.py:206, in open(sequence, **kwargs)
204 warn(message)
205 exceptions += message + '\n'
--> 206 raise UnknownFormatError("All handlers returned exceptions:\n" + exceptions)

UnknownFormatError: All handlers returned exceptions:
<class 'pims.bioformats.BioformatsReader'> errored: 'NoneType' object has no attribute 'isJVMStarted'

Your help would be much appreciated!!

[nimaesmaeelpour]

The problem is that jpype is not installed.

The jpype variable becomes a NoneType and the error is raised.

pims/pims/bioformats.py

Lines 8 to 11 in 5ec734d

	try:
	import jpype
	except ImportError:
	jpype = None

But after installing jpype, a completely different problem opens up. The loci_tools.jar can't be downloaded.

pims/api.py:204: UserWarning: <class 'pims.bioformats.BioformatsReader'> errored: HTTP Error 404: Not Found
  warn(message)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
File "pims/api.py", line 206, in open
    raise UnknownFormatError("All handlers returned exceptions:\n" + exceptions)
pims.api.UnknownFormatError: All handlers returned exceptions:
<class 'pims.bioformats.BioformatsReader'> errored: HTTP Error 404: Not Found

I think this url is outdated (at least with version 6, which is the default value for version):

pims/pims/bioformats.py

Lines 74 to 75 in 5ec734d

	url = ('http://downloads.openmicroscopy.org/bio-formats/' + version +
	'/artifacts/loci_tools.jar')

Right now the workaround is to install pims-nd2which uses the Nikon SDK to open nd2-files.