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

[Thomas Julou]

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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