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

[Thomas Julou]

Dear Curtis,

thanks for your answer.
In fact, I’m not sure whether it’s more a scifio issue or a fiji one. My point is that in the fiji interface, open parses all positions although it opens a single file. 

Does scifio aim at handling entire datasets? then I understands that it has the ability to parse entire datasets, but the way it’s called by fiji could probably be significantly more efficient. or at least open a bioformat-like dialog offering to open all positions.
If scifio is designed with single images, then its code could probably be stripped down to parse metadata more efficiently…

Best,
Thomas



> On 12 Aug 2015, at 00:14, Curtis Rueden <ctrueden at wisc.edu> wrote:
> 
> 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 <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 <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 <mailto: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 <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 <http://micro-manager.3463995.n2.nabble.com/BigTiff-support-tt7580735.html#a7585743>
> _______________________________________________
> SCIFIO mailing list
> SCIFIO at scif.io <mailto:SCIFIO at scif.io>
> http://scif.io/mailman/listinfo/scifio <http://scif.io/mailman/listinfo/scifio>
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20150812/5df1d68e/attachment.html>