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fiji / Stitching

Fiji's Stitching plugins reconstruct big images from tiled input images.
http://imagej.net/Stitching
GNU General Public License v2.0
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Cannot open other file format than LOCI #19

Open jejmule opened 10 years ago

jejmule commented 10 years ago

I am using the plugin in ImageJ

I have implemented a reader for my specific file format : using HandleExtraFileTypes to enable native recognition of the image in ImageJ. I can drag and drop iage for opening.

The file format is recognized by ImageJ but cannot be open by the stitching plugin.

hinerm commented 10 years ago

@jejmule - Stitching uses Bio-Formats for image importing (see this line of Stitching_Grid) which is why your reader is not being used.

I got your private e-mail about creating a SCIFIO reader for your format. I was just going to write a response to it on the SCIFIO mailing list.

If you were to implement your reader as a SCIFIO format, then I would have an excellent use case to work on https://github.com/scifio/scifio-bf-compat/issues/4, which would allow your format to be picked up by the Stitching plugin.

dscho commented 10 years ago

@hinerm actually, the Stitching plugin should switch from Bio-Formats to SCIFIO already.

hinerm commented 10 years ago

@dscho to clarify, do you mean "we should rewrite Stitching to use SCIFIO" or "it already is using SCIFIO"?

glancing at the repo, I don't see how the latter is possible.. please correct me if I'm wrong though.

ctrueden commented 10 years ago

@hinerm I think he means the former. But actually, I am not sure yet... the SCIFIO API is still in flux, and the more things we update to use it right now, the more maintenance burden it becomes later as we ramp up toward SCIFIO 1.0.0. I would be more in favor of switching Stitching over to SCIFIO after a SCIFIO 1.0.0 release. In which case, your plan to use scifio-bf-compat in the other direction in the meantime makes total sense to me.

dscho commented 10 years ago

@dscho @hinerm yep, I meant "Stitching should be rewritten to use SCIFIO".

And just to clarify: I was not proposing that us three take on even more tasks than we already have weighing down on our shoulders. It would be a perfect opportunity to bring @StephanPreibisch in – whose project this is, after all, so it would be improper for us to take control of it (and it would also fly in the face of Fiji's community project nature). Also, that way SCIFIO would most likely benefit from it because it will show rough edges in the API that still need to be filed down.

dscho commented 10 years ago

And to make sure that we give @StephanPreibisch a chance to prevent us infamous three from interfering with his wishes, I just opened #20.