According to the docs in http://pythonhosted.org//python-bioformats/ I should be able to do

pip install python-bioformats

I tried it using virtualenv and I get the following

(bioformats)cmu-883713:src icaoberg$ pip install python-bioformats
Downloading/unpacking python-bioformats
  Could not find a version that satisfies the requirement python-bioformats (from versions: 1.0.0pr1, 1.0.0pr2, 1.0.0pr3)
Cleaning up...
No distributions matching the version for python-bioformats
Storing debug log for failure in /Users/icaoberg/.pip/pip.log

I have no idea how hard this is, but I'm in the "Python 3" birds-of-a-feather session at SciPy 2014 and realised this is one of the only libraries I use that is not Python 3 compatible.

(or, at the very least, "pip install python-bioformats" works for me in 2 envs but not 3.)

Hi guys,

since today I have a seroius problem on my Windows7 64bit machine. I use javabrige 1.0.9, bioformats 1.0.4 and bioformats_package 5.0.8. Until Friday this worked fine but since today I get:

Python 2.7.9 (default, Dec 10 2014, 12:28:03) [MSC v.1500 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

import javabridge as jv import bioformats path = r'C:\Users\M1SRH\Documents\Software\Bio-Formats_Package\5.0.8\bioformats_package.jar' jars = jv.JARS + [path] jv.start_vm(class_path=jars, max_heap_size='2G') imagefile = r'C:\Users\M1SRH\Documents\Spyder_Projects_Testdata\CZI_Read\XYZCT_Z=15_C=2_T=20.czi' rdr = bioformats.get_image_reader(None, path=imagefile) Failed to get class loci/common/RandomAccessInputStream java.lang.NoClassDefFoundError: loci/common/RandomAccessInputStream Caused by: java.lang.ClassNotFoundException: loci.common.RandomAccessInputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:372) at java.net.URLClassLoader$1.run(URLClassLoader.java:361) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:360) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) Traceback (most recent call last): File "", line 1, in File "C:\Python27\lib\site-packages\bioformats\formatreader.py", line 900, in get_image_reader rdr = ImageReader(path=path, url=url) File "C:\Python27\lib\site-packages\bioformats\formatreader.py", line 621, in init self.path) File "C:\Python27\lib\site-packages\javabridge\jutil.py", line 1655, in make_instance raise JavaException(jexception) javabridge.jutil.JavaException: loci/common/RandomAccessInputStream

The sample dataset used can be downloaded here:

https://www.dropbox.com/s/fu4ijim5a4n8tka/XYZCT_Z%3D15_C%3D2_T%3D20.czi?dl=0

I hope you can find the problem soon ... Let me know, if you need more infor or help.

Sebi

Hi,

I have a 383GB Leica .lif file, which obviously I would like to process sequentially. (It contains a large number of 1024 x 1024 x 30 x 3channel images.) I figured I would read the metadata and then use bioformats.load_image with the right parameters to load each image series. (Incidentally, it would be great to allow z=None to load up the entire stack! Happy to submit a PR if that would be welcome and you can point me in the right direction!)

Here's my code snippet:

import javabridge as jv
import bioformats as bf
jv.start_vm(class_path=bf.JARS)
md = bf.get_omexml_metadata('Long time Gfap 260314.lif')

And here's the resulting error:

---------------------------------------------------------------------------
JavaException                             Traceback (most recent call last)
<ipython-input-7-640f92a788d5> in <module>()
----> 1 md = bf.get_omexml_metadata('Long time Gfap 260314.lif')

/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/bioformats/formatreader.pyc in get_omexml_metadata(path, url)
    943         xml;
    944         """
--> 945         xml = jutil.run_script(script, dict(path=rdr.path, reader = rdr.rdr))
    946         return xml

/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/javabridge/jutil.pyc in run_script(script, bindings_in, bindings_out, class_loader)
    338              "Ljava/lang/Object;)"
    339              "Ljava/lang/Object;",
--> 340              scope, script, "<java-python-bridge>", 0, None)
    341         result = unwrap_javascript(result)
    342         for k in list(bindings_out):

/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/javabridge/jutil.pyc in call(o, method_name, sig, *args)
    888     ret_sig = sig[sig.find(')')+1:]
    889     nice_args = get_nice_args(args, args_sig)
--> 890     result = fn(*nice_args)
    891     x = env.exception_occurred()
    892     if x is not None:

/Users/nuneziglesiasj/anaconda/lib/python2.7/site-packages/javabridge/jutil.pyc in fn(*args)
    855             x = env.exception_occurred()
    856             if x is not None:
--> 857                 raise JavaException(x)
    858             return result
    859     else:

JavaException: Java heap space

What's the correct way to use python-bioformats to read in a file one series at a time? Or is such functionality not currently supported?

Thanks!

Dear Mr. Kamentsky, I encountered an error when running my python with bioformats:

jmd = jv.JWrapper(rdr.rdr.getMetadataStore()) AttributeError: 'ImageReader' object has no attribute 'rdr'

I could find ImageReader class in formatreader.py under the folder \site-packages\bioformats, but no attribute 'rdr' there. If I ran it in command line, I got error as follows:

File "C:\Program Files\Anaconda\Lib\site-packages\javabridge\wrappers.py", line 81, in getattr raise AttributeError()

If I run test macro as follows:

import os import javabridge as jv paths = jv.JClassWrapper('java.lang.System').getProperty('java.class.path').split(";") for path in paths: print "%s: %s" %("exists" if os.path.isfile(path) else "missing", path)

I can get:

exists: C:\Program Files\Anaconda\lib\site-packages\javabridge\jars\rhino-1.7R4.jar exists: C:\Program Files\Anaconda\lib\site-packages\javabridge\jars\runnablequeue.jar exists: C:\Program Files\Anaconda\lib\site-packages\javabridge\jars\cpython.jar exists: C:\Users\zcjitang\Documents\Software\Bioformats\bioformats_package_5.1.1.jar

Then I do not know what's wrong with it. Could you help? Thank you very much. I had installed the latest PyWin32, Bioformats, Javabridge, vLFD, Numpy and matplotlib based on my requirements from http://www.lfd.uci.edu/~gohlke/pythonlibs/.

Here's a tentative implementation of Python3 support (closes #12 and #51).

All of the nosetests are currently passing with Python 2.7.10 and Python 3.5.0 (I also fixed a minor issue that was causing failures in the OME XML tests), although there might be a few remaining incompatibilities that I've missed.

Hi,

I have a 50 GB Nikon nd2 file with 1000 frames of dimensions 101x512x512, and I do my image analysis by iterate over the frames using a code that boils down to:

for t in range(sizeT):
    for z in range(sizeZ):
        index = reader.rdr.getIndex(z, c, t)
        image[z]= reader.read(series=0, index=index, rescale=False)
    # some analysis

I start my VM with 512MB heap space like this:

javabridge.start_vm(class_path=bioformats.JARS, max_heap_size='512m')
javabridge.attach()

About halfway the t-loop, I get JavaException: GC overhead limit exceeded. Are there extra things I could do to free memory?

Python stack:

C:\Anaconda\lib\site-packages\bioformats\formatreader.pyc in read(self, c, z, t, series, index, rescale, wants_max_intensity, channel_names)
    775             dtype = '<f8' if little_endian else '>f8'
    776             scale = 1
--> 777         max_sample_value = self.rdr.getMetadataValue('MaxSampleValue')
    778         if max_sample_value is not None:
    779             try:

C:\Anaconda\lib\site-packages\javabridge\jutil.pyc in method(self, *args)
    897     def method(self, *args):
    898         assert isinstance(self.o, _javabridge.JB_Object)
--> 899         result = call(self.o, name, sig, *args)
    900         if fn_post_process is not None:
    901             result = fn_post_process(result)

C:\Anaconda\lib\site-packages\javabridge\jutil.pyc in call(o, method_name, sig, *args)
    828     ret_sig = sig[sig.find(')')+1:]
    829     nice_args = get_nice_args(args, args_sig)
--> 830     result = fn(*nice_args)
    831     x = env.exception_occurred()
    832     if x is not None:

C:\Anaconda\lib\site-packages\javabridge\jutil.pyc in fn(*args)
    795             x = env.exception_occurred()
    796             if x is not None:
--> 797                 raise JavaException(x)
    798             return result
    799     else:

 JavaException: GC overhead limit exceeded

Java stack:

java.lang.OutOfMemoryError: GC overhead limit exceeded
at loci.formats.FormatReader.updateMetadataLists(FormatReader.java:413)
at loci.formats.FormatReader.flattenHashtables(FormatReader.java:405)
at loci.formats.FormatReader.getMetadataValue(FormatReader.java:1065)

Hello! I think that something went wrong in 2eae542835e4d6ec7e133238cf289b987fcbcfce (the python 3 string handling commit); we were hitting encoding errors reading metadata like m = get_omexml_metadata("my_file.oif"); o = OMEXML(m).

The exception was being thrown from here: https://github.com/CellProfiler/python-bioformats/blame/master/bioformats/omexml.py#L318-L320

For the m we were getting back, type(m) was unicode and ElementTree was choking on it. If we passed m.encode('utf-8') into OMEXML(), our XML was getting encoded a second time, and the second encode choked.

The prior version of the conditional was if isinstance(xml, unicode); after making that change locally, our images processed fine. I'm not sure how you'd prefer to finesse that to make it py3k-friendly. :)

/cc @alimuldal @hsiehj6

How this works.

• Try to handle Python and related dependencies with conda. Makes it really easy to install numpy and the sort. Also, uses binaries so it is really fast (no build time). Usually, has recent versions.
• Uses a Java language environment. It is needed for some things in here anyways. Also, the Travis Python environment would be replaced with conda's so we don't care about it.
• Use pip to install the latest python-javabridge. Easy to do. Likely what someone will do when installing themselves.
• Builds the sphinx docs with the html target. Just verifies the docs can still be built. May provide elucidating warnings in-case somebody isn't following correct syntax.
• Provides some coverage setting. Could be used to report to coveralls.io given some tweaks to python-javabridge.

Hi guys,

I just tried to test the python-bioformats library and got stuck with I problem. I am not a programmer, so my question might be silly ... When I open the file inside Fiji using the BioFormats Importer it works fine, so the file itself is ok. And I also managed to read it using: http://www.lfd.uci.edu/~gohlke/pythonlibs/#bioformats

But when I use python-bioformats I get those error messages:

java.lang.IllegalArgumentException: 0.0 must not be null and positive. at ome.xml.model.primitives.PositiveFloat.(PositiveFloat.java:41) at loci.formats.in.MRCReader.initFile(MRCReader.java:286) at loci.formats.FormatReader.setId(FormatReader.java:1072) java.lang.NoClassDefFoundError: Glacier2/PermissionDeniedException Caused by: java.lang.ClassNotFoundException: Glacier2.PermissionDeniedException at java.net.URLClassLoader$1.run(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) Traceback (most recent call last): File "", line 1, in File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 908, in load_using_bioformats with ImageReader(path=path) as rdr: File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 634, in init self.init_reader() File "C:\Python27\lib\site-packages\python_bioformats-0.0.0-py2.7.egg\bioformats\formatreader.py", line 675, in init_reader je, "Glacier2/PermissionDeniedException"): File "C:\Python27\lib\site-packages\javabridge\jutil.py", line 811, in is_instance_of raise JavaException(jexception) javabridge.jutil.JavaException: Glacier2/PermissionDeniedException

Thanks for the help,

Sebastian

It appears version information used to be in another file ( https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/init.py#L13 ). However, that file does not appear to exist. Also, it looks like python-javabridge has the same issue.

Hi, if I got a series of the top left coordinates (x, y) of size with (500 x 500) images and use openBytesXYWH(0, x, y, 500, 500). to extract the images, how can I get them with multiprocessing in python?

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 python-bioformats. As it is not necessary for the core of the library i was wondering if you would consider making this dependency optional and factoring out the logic to connect to s3 and omero?

I am also happy to provide a PR !

I am trying to analyze a .ch5 (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). How can I resolve this error, or is there a better way to analyze .ch5 files with python? The output of the code is below. Thanks!

14:47:09.187 [Thread-0] DEBUG loci.formats.FormatHandler - NDPISReader initializing /home/roshankern/Desktop/NucleusMorphology/phenotypic_profiling/idr_downloads/test.ch5 14:47:09.187 [Thread-0] DEBUG loci.formats.FormatHandler - loci.formats.in.NDPISReader.initFile(/home/roshankern/Desktop/NucleusMorphology/phenotypic_profiling/idr_downloads/test.ch5)

---

JavaException Traceback (most recent call last) ... JavaException: <Java object at 0x19f14798> During handling of the above exception, another exception occurred: OSError Traceback (most recent call last) ... OSError: [Errno 22] Could not load the file as an image (see log for details): b'/home/roshankern/Desktop/NucleusMorphology/phenotypic_profiling/idr_downloads/test.ch5'

CC @gwaygenomics to keep you in the loop

On the https://pythonhosted.org/python-bioformats/, the provided link for the OME-XML schema documentation is outdated. The correct link is the following: (https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html).

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" all frames within a multidimensional image as Timepoints instead of C, Z and T series. Example files can be found here for testing.

The core issue was that python-bioformats used a custom strategy in get_image_reader to attempt to find the correct reader for a supplied image file. This involved testing filenames against the list of available reader classes over a series of passes aimed at finding the best match. The key objective there was to avoid needing to have bioformats open the files and inspect the header to determine whether said reader was the correct choice, instead basing things on the file extension if possible.

However, the reader selection implementation in bioformats has evolved substantially over the years. Today the OME-TIF reader (for example) will never be selected at all if performing selection in extension-only mode. Extension-only matching is actually now also available as an option within the reader, so the javascript implementation from python-bioformats is somewhat redundant. Furthermore, allowing bioformats to open files for inspection is no longer associated with the same performance cost that it once was. In my testing allowing file inspection resulted in CellProfiler getting the correct reader and metadata without any significant slowdown.

With this in mind, I've revised the reader selection function to use the native bioformats selector, with the option to work in extension-only mode parameterised as the new allow_open_image argument in get_image_reader. I've had this default to True to ensure that the correct reader is selected by default.

In a seperate PR we should add a CellProfiler setting to revert back to the old functionality, which would basically pass allow_open_image=False into reader requests. This would deliver the same results as the current release so that anyone who wrote their pipeline to handle the incorrect metadata can still use those workflows.

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 not find loci.formats.in.URLReader
java.lang.ClassNotFoundException: loci.formats.in.URLReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) ~[na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
09:04:19.677 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.SlideBook6Reader
java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) ~[na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
09:04:19.677 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ScreenReader
java.lang.ClassNotFoundException: loci.formats.in.ScreenReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) ~[na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
09:04:19.677 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ZarrReader
java.lang.ClassNotFoundException: loci.formats.in.ZarrReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) ~[na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
09:04:19.881 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.URLReader
java.lang.ClassNotFoundException: loci.formats.in.URLReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) [na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) [na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:122) [bioformats_package.jar:6.6.0]
	at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80) [bioformats_package.jar:6.6.0]
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:67) [bioformats_package.jar:6.6.0]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.8.0_312]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) [na:1.8.0_312]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.8.0_312]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [na:1.8.0_312]
	at java.lang.Class.newInstance(Class.java:442) [na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_312]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_312]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_312]
	at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:225) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.optimizer.OptRuntime.callProp0(OptRuntime.java:85) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1._c_script_0(<java-python-bridge>:6) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.exec(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.Context.evaluateString(Context.java:1079) [rhino-1.7R4.jar:1.7R4]
09:04:19.881 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.SlideBook6Reader
java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) [na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) [na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:122) [bioformats_package.jar:6.6.0]
	at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80) [bioformats_package.jar:6.6.0]
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:67) [bioformats_package.jar:6.6.0]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.8.0_312]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) [na:1.8.0_312]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.8.0_312]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [na:1.8.0_312]
	at java.lang.Class.newInstance(Class.java:442) [na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_312]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_312]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_312]
	at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:225) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.optimizer.OptRuntime.callProp0(OptRuntime.java:85) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1._c_script_0(<java-python-bridge>:6) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.exec(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.Context.evaluateString(Context.java:1079) [rhino-1.7R4.jar:1.7R4]
09:04:19.882 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ScreenReader
java.lang.ClassNotFoundException: loci.formats.in.ScreenReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) [na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) [na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:122) [bioformats_package.jar:6.6.0]
	at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80) [bioformats_package.jar:6.6.0]
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:67) [bioformats_package.jar:6.6.0]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.8.0_312]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) [na:1.8.0_312]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.8.0_312]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [na:1.8.0_312]
	at java.lang.Class.newInstance(Class.java:442) [na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_312]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_312]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_312]
	at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:225) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.optimizer.OptRuntime.callProp0(OptRuntime.java:85) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1._c_script_0(<java-python-bridge>:6) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.exec(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.Context.evaluateString(Context.java:1079) [rhino-1.7R4.jar:1.7R4]
09:04:19.882 [Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ZarrReader
java.lang.ClassNotFoundException: loci.formats.in.ZarrReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418) ~[na:1.8.0_312]
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) ~[na:1.8.0_312]
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ~[na:1.8.0_312]
	at java.lang.Class.forName0(Native Method) [na:1.8.0_312]
	at java.lang.Class.forName(Class.java:264) [na:1.8.0_312]
	at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package.jar:6.6.0]
	at loci.formats.ClassList.<init>(ClassList.java:122) [bioformats_package.jar:6.6.0]
	at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80) [bioformats_package.jar:6.6.0]
	at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:67) [bioformats_package.jar:6.6.0]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.8.0_312]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) [na:1.8.0_312]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [na:1.8.0_312]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [na:1.8.0_312]
	at java.lang.Class.newInstance(Class.java:442) [na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_312]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_312]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_312]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_312]
	at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:225) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.optimizer.OptRuntime.callProp0(OptRuntime.java:85) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1._c_script_0(<java-python-bridge>:6) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091) [rhino-1.7R4.jar:1.7R4]
	at org.mozilla.javascript.gen._java_python_bridge__1.call(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.gen._java_python_bridge__1.exec(<java-python-bridge>) [rhino-1.7R4.jar:na]
	at org.mozilla.javascript.Context.evaluateString(Context.java:1079) [rhino-1.7R4.jar:1.7R4]
09:04:19.897 [Thread-0] DEBUG o.s.nativelib.NativeLibraryUtil - processor is INTEL_64 os.arch is amd64
09:04:19.897 [Thread-0] DEBUG o.s.nativelib.NativeLibraryUtil - architecture is LINUX_64 os.name is linux
09:04:19.898 [Thread-0] DEBUG o.s.nativelib.NativeLibraryUtil - architecture is LINUX_64 os.name is linux
09:04:19.898 [Thread-0] DEBUG o.s.nativelib.NativeLibraryUtil - platform specific path is META-INF/lib/linux_64/
09:04:19.898 [Thread-0] DEBUG o.scijava.nativelib.BaseJniExtractor - mappedLib is libturbojpeg.so
09:04:19.898 [Thread-0] DEBUG o.scijava.nativelib.BaseJniExtractor - URL is jar:file:/home/vbmade2000/Documents/new_oa/bioformat/venv/lib/python3.8/site-packages/bioformats/jars/bioformats_package.jar!/META-INF/lib/linux_64/libturbojpeg.so
09:04:19.898 [Thread-0] DEBUG o.scijava.nativelib.BaseJniExtractor - URL path is file:/home/vbmade2000/Documents/new_oa/bioformat/venv/lib/python3.8/site-packages/bioformats/jars/bioformats_package.jar!/META-INF/lib/linux_64/libturbojpeg.so
09:04:19.902 [Thread-0] DEBUG o.scijava.nativelib.BaseJniExtractor - Extracting 'jar:file:/home/vbmade2000/Documents/new_oa/bioformat/venv/lib/python3.8/site-packages/bioformats/jars/bioformats_package.jar!/META-INF/lib/linux_64/libturbojpeg.so' to '/tmp/libturbojpeg4805853447258276507.so'
09:04:19.968 [Thread-0] DEBUG loci.common.services.ServiceFactory - Loaded properties from: services.properties
09:04:19.968 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.POIService and implementation class loci.formats.services.POIServiceImpl
09:04:19.968 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MDBService and implementation class loci.formats.services.MDBServiceImpl
09:04:19.968 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JPEGTurboService and implementation class loci.formats.services.JPEGTurboServiceImpl
09:04:19.969 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface ome.codecs.services.LuraWaveService and implementation class ome.codecs.services.LuraWaveServiceImpl
09:04:19.969 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.common.services.S3ClientService and implementation class loci.common.services.S3ClientServiceImpl
09:04:19.969 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JAIIIOService and implementation class loci.formats.services.JAIIIOServiceImpl
09:04:19.969 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.WlzService and implementation class loci.formats.services.WlzServiceImpl
09:04:19.970 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JHDFService and implementation class loci.formats.services.JHDFServiceImpl
09:04:19.970 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.NetCDFService and implementation class loci.formats.services.NetCDFServiceImpl
09:04:19.970 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.EXIFService and implementation class loci.formats.services.EXIFServiceImpl
09:04:19.970 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MetakitService and implementation class loci.formats.services.MetakitServiceImpl
09:04:19.970 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.LuraWaveService and implementation class loci.formats.services.LuraWaveServiceImpl
09:04:19.971 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.OMEXMLService and implementation class loci.formats.services.OMEXMLServiceImpl
09:04:19.971 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface ome.codecs.services.JAIIIOService and implementation class ome.codecs.services.JAIIIOServiceImpl
09:04:19.971 [Thread-0] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.JPEGXRService and implementation class loci.formats.services.JPEGXRServiceImpl
09:04:19.991 [Thread-0] DEBUG loci.formats.FormatHandler - TiffReader initializing /tmp/MOSA-PHH-04_11_T0001F001L01A01Z01C01.tif
09:04:19.991 [Thread-0] DEBUG loci.formats.FormatHandler - loci.formats.in.TiffReader.initFile(/tmp/MOSA-PHH-04_11_T0001F001L01A01Z01C01.tif)
09:04:19.993 [Thread-0] INFO  loci.formats.in.MinimalTiffReader - Reading IFDs
09:04:20.003 [Thread-0] INFO  loci.formats.in.MinimalTiffReader - Populating metadata
09:04:20.009 [Thread-0] INFO  loci.formats.in.TiffReader - Checking comment style
09:04:20.009 [Thread-0] INFO  loci.formats.in.BaseTiffReader - Populating OME metadata
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Invalid timestamp '20210204 11:17:35.363' for current locale
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Could not parse timestamp '20210204 11:17:35.363' with EN_US locale
java.lang.IllegalArgumentException: Invalid format: "20210204 11:17:35" is malformed at " 11:17:35"
	at org.joda.time.format.DateTimeFormatter.parseDateTime(DateTimeFormatter.java:871) ~[bioformats_package.jar:6.6.0]
	at org.joda.time.Instant.parse(Instant.java:98) ~[bioformats_package.jar:6.6.0]
	at loci.common.DateTools.parseDate(DateTools.java:291) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:357) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:432) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:416) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:430) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:236) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:586) [bioformats_package.jar:6.6.0]
	at loci.formats.FormatReader.setId(FormatReader.java:1421) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffDelegateReader.setId(TiffDelegateReader.java:92) [bioformats_package.jar:6.6.0]
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Invalid timestamp '20210204 11:17:35.363' for current locale
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Could not parse timestamp '20210204 11:17:35.363' with EN_US locale
java.lang.IllegalArgumentException: Invalid format: "20210204 11:17:35" is malformed at "210204 11:17:35"
	at org.joda.time.format.DateTimeFormatter.parseDateTime(DateTimeFormatter.java:871) ~[bioformats_package.jar:6.6.0]
	at org.joda.time.Instant.parse(Instant.java:98) ~[bioformats_package.jar:6.6.0]
	at loci.common.DateTools.parseDate(DateTools.java:291) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:357) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:432) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:416) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:430) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:236) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:586) [bioformats_package.jar:6.6.0]
	at loci.formats.FormatReader.setId(FormatReader.java:1421) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffDelegateReader.setId(TiffDelegateReader.java:92) [bioformats_package.jar:6.6.0]
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Invalid timestamp '20210204 11:17:35.363' for current locale
09:04:20.010 [Thread-0] DEBUG loci.common.DateTools - Could not parse timestamp '20210204 11:17:35.363' with EN_US locale
java.lang.IllegalArgumentException: Invalid format: "20210204 11:17:35" is malformed at "210204 11:17:35"
	at org.joda.time.format.DateTimeFormatter.parseDateTime(DateTimeFormatter.java:871) ~[bioformats_package.jar:6.6.0]
	at org.joda.time.Instant.parse(Instant.java:98) ~[bioformats_package.jar:6.6.0]
	at loci.common.DateTools.parseDate(DateTools.java:291) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:357) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:432) [bioformats_package.jar:6.6.0]
	at loci.common.DateTools.formatDate(DateTools.java:416) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadataStore(BaseTiffReader.java:430) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffReader.initMetadataStore(TiffReader.java:236) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98) [bioformats_package.jar:6.6.0]
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:586) [bioformats_package.jar:6.6.0]
	at loci.formats.FormatReader.setId(FormatReader.java:1421) [bioformats_package.jar:6.6.0]
	at loci.formats.in.TiffDelegateReader.setId(TiffDelegateReader.java:92) [bioformats_package.jar:6.6.0]
09:04:20.012 [Thread-0] DEBUG loci.formats.FormatTools - Expected positive value for PhysicalSize; got 0.0
09:04:20.012 [Thread-0] DEBUG loci.formats.FormatTools - Expected positive value for PhysicalSize; got 0.0

Is there a way to suppress/resolve this?