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fiji / SPIM_Registration

Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher
GNU General Public License v2.0
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Fixes to SlideBook SLD file reader #114

Closed RichardMyers closed 7 years ago

RichardMyers commented 7 years ago

Fixed SlideBook SLD file image,channel,angle naming to make it work with scripts; also fixed reading multichannel sld files

ctrueden commented 7 years ago

It concerns me to see all this effort being done on another SLD reader that is not the Bio-Formats reader, and is not SCIFIO-based. What is the long term plan here?

RichardMyers commented 7 years ago

This plugin has custom readers for a handful of file formats (eg. LightSheet Z1), but there does not appear to be a way to generically read all file formats supported by Bio-Formats. We would certainly prefer to use a more generic Bio-Formats based system if one existed.

ctrueden commented 7 years ago

there does not appear to be a way to generically read all file formats supported by Bio-Formats. We would certainly prefer to use a more generic Bio-Formats based system if one existed.

You certainly can read data agnostically using the Bio-Formats API, via the loci.formats.ImageReader class. There is lots of documentation.

I know that @StephanPreibisch is familiar with this API, having used it in the past.

If there is something I'm missing here, please let me know.

RichardMyers commented 7 years ago

@ctrueden When I began this project with @StephanPreibisch the bio-formats project was planned to include SlideBook6Reader directly. Later, as you mentioned in fiji/SPIM_Registration/pull/115, it was decided that the SlideBook6Reader should be moved to be an external project that is late loaded, as per openmicroscopy/bioformats/pull/2496.

As you suggest above, the correct way forward is to make the required changes to the SPIM_Registration plugin to load SlideBook6 files using the loci.formats.ImageReader infrastructure, similar to how the LightSheetZ1 reader operates.

I am not as experienced with Java or the Bioformats/ImageJ universe of inter-related technologies as I should be, which is why I went with the simpler direct method originally. I'll give it a try, but I appreciate your understanding that this is a non-trivial change for me to make.

StephanPreibisch commented 7 years ago

Hi @RichardMyers @ctrueden, I think Curtis and me should discuss the long-term strategy at the NEUBIAS meeting in Lisbon. I will merge this request for now to move forward. Thanks a lot, Stephan