3i Slidebook Reader

[evamaxfield]

Use Case

Please provide a use case to help us understand your request in context AICS gene editing using 3i scopes for some imaging. These scopes produce .sld or slidebook files. Would be nice to be able to read all of AICS produced imaging data under one library.

Solution

Please describe your ideal solution I think @heeler talked about writing the module in C++ just like aicspylibczi. But we should first look around for other libraries that can read 3i. If there are none, I say we should take this as an opportunity to try out rust development.

Alternatives

Please describe any alternatives you've considered, even if you've dismissed them

[toloudis]

Some info / clues to reference implementations: https://forum.image.sc/t/sld-bio-formats-errors/48353

Supposedly Slidebook has a "export OME TIFF" but I'm not sure whether it's automatable. Will have to check w/microscopists.

[jni]

Hi all, has anyone made any progress here, that might not be pushed to the latest main?

[toloudis]

Some progress has been made. We don't have a complete implementation that is ready yet but there are some plans in motion to arrive at a working (maybe non optimal) solution, and some later plans to get a more optimal solution.

[evamaxfield]

@toloudis can we try to get somone from AICS to try 4.2 with a SLD file? Would love to close this.

[evamaxfield]

Actually I will tag @cfrick13. If you get a chance can you test a slidebook file?

[cfrick13]

I tried multiple slidebook files and they currently do not work with the aicsimageio==4.2.0

[evamaxfield]

I tried multiple slidebook files and they currently do not work with the aicsimageio==4.2.0

Mind sending us the files in dropbox or similar?

[cfrick13]

from aicsimageio.readers import bioformats_reader

bf_reader = bioformats_reader.BioformatsReader(r"20210428_T02_002.sld")

---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\_jpype.cp38-win_amd64.pyd in loci.formats.ImageReader.setId()

~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\_jpype.cp38-win_amd64.pyd in loci.formats.FormatReader.setId()

~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\_jpype.cp38-win_amd64.pyd in loci.formats.in.SlidebookReader.initFile()

Exception: Java Exception

The above exception was the direct cause of the following exception:

java.lang.ArrayIndexOutOfBoundsException  Traceback (most recent call last)
~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\aicsimageio\readers\bioformats_reader.py in __init__(self, image, original_meta, memoize, options)
    108         try:
--> 109             with BioFile(self._path, **self._bf_kwargs) as rdr:  # type: ignore
    110                 md = rdr._r.getMetadataStore()

~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\aicsimageio\readers\bioformats_reader.py in __init__(self, path, series, meta, original_meta, memoize, options)
    279 
--> 280         self.open()
    281         self._lock = Lock()

~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\aicsimageio\readers\bioformats_reader.py in open(self)
    308         """Open file."""
--> 309         self._r.setId(self._path)
    310 

java.lang.ArrayIndexOutOfBoundsException: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0

During handling of the above exception, another exception occurred:

UnsupportedFileFormatError                Traceback (most recent call last)
C:\Users\CHRIS~1.FRI\AppData\Local\Temp/ipykernel_17988/2797730550.py in <module>
      2 # 'sld': ['aicsimageio.readers.bioformats_reader.BioformatsReader'],
      3 
----> 4 bf_reader = bioformats_reader.BioformatsReader(r"\\allen\aics\assay-dev\MicroscopyData\John Paul\2021\20210428\20210428_T02_002.sld")

~\AppData\Local\Continuum\anaconda3\envs\aics_bf2\lib\site-packages\aicsimageio\readers\bioformats_reader.py in __init__(self, image, original_meta, memoize, options)
    115             raise
    116         except Exception:
--> 117             raise exceptions.UnsupportedFileFormatError(
    118                 self.__class__.__name__, self._path
    119             )

UnsupportedFileFormatError: BioformatsReader does not support the image: '20210428_T02_002.sld'.

[tlambert03]

yeah, i'm not surprised to hear this. 3i took control of their own bioformats plugin, so it's not included with the bioformats_jar. we'll need to handle this case specially (and I'm not sure what the deal with distribution of 3i's jar is)

[tlambert03]

Mind sending us the files in dropbox or similar?

but, it would be handy to have a sample!

[cfrick13]

I slacked a .sld file to dan and jackson (faster than me trying to clean out my old dropbox). Hope that works. Excited to see .sld support soon hopefully :)

[joshmoore]

I'm not sure what the deal with distribution of 3i's jar is

see https://www.intelligent-imaging.com/technical-answers and http://sites.imagej.net/SlideBook/

[tlambert03]

@joshmoore ... don't see any clear license info there. do you have any insight on that?

[joshmoore]

cc: @RichardMyers (https://github.com/ome/bioformats/pull/2289)

[SeanDuHare]

Closing this as duplicate of this slightly more recent issue #428