[SCIFIO] Open Micro-Manager dataset in Fiji using SCIFIO

[Curtis Rueden]

Hi Thomas,

Thanks for the report. I filed an issue in the SCIFIO issue tracker with
these details:

https://github.com/scifio/scifio/issues/279

Things are crazy busy until the ImageJ conference this September, but we
will try to respond more thoroughly later this fall.

In the meantime, in case you didn't already know, the relevant source code
is here:
https://github.com/scifio/scifio/blob/scifio-0.24.0/src/main/java/io/scif/formats/MicromanagerFormat.java

Be warned that SCIFIO is undergoing a substantial refactoring at the
moment, to move away from plane-centric API toward a block-based one.

Regards,
Curtis

On Fri, Aug 7, 2015 at 3:34 AM, Thomas Julou <thomas.julou at normalesup.org>
wrote:

> Hello,
>
> In line with earlier posts on ome-users mailing list [1], I’m trying to
> find a convenient way to open large Micro-Manager stacks in Fiji (in
> particular, such stacks are split in several 4.2gb tif files because MM
> doesn’t handle bigtiff). My problem so far has been that Bio-formats is
> parsing all positions in a dataset even when opening a single one. Mark
> Tsuchida (MM’s developer) suggested that using SCIFIO might be a workaround
> [2].
>
> I tried the following:
> - File > Import > SCIFIO
> This raises an exception and open an error dialog… You might want to fix
> this, unless it’s a fiji specific issue…
> - File > Open after selecting “Use SCIFIO” in Options > ImageJ2
> This successfully opens the file but it’s slower than the File > Import >
> BioFormats! Moreover it parses metadata for all positions in the dataset
> (even when they are saved to different files). I can’t understand this
> behaviour since there is no way to choose to open all related positions… In
> my opinion the appropriate behaviour would be: if the MM dataset is saved
> with all positions in the same stack (i.e. no “_Posxx.ome.tif” in the file
> name; possibly split in several .tif files) then open each position in a
> separate window, if the MM dataset is saved with positions in separate
> files (i.e. “_Posxx.ome.tif” found in the file name; again possibly split
> in several .tif files if a given position is larger than 4.2gb) then ***parse
> only*** and open only the selected position… This would really speed
> things up for stacks acquired in datasets with many positions (of a few
> large ones).
>
> I hope that this makes sense and that the issue can be addressed.
> Thanks for your help. Best,
>
> Thomas
>
> [1]
> http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005101.html
> [2]
> http://micro-manager.3463995.n2.nabble.com/BigTiff-support-tt7580735.html#a7585743
>
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>
>
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