Closed CellKai closed 1 year ago
Hi, I just implemented the support to create multi-resolution outputs for fused HDF5/N5/ZARR images. Simply update Fiji and check “create multi-resolution pyramid” during fusion (see screenshot).
Please let me know if that works (it does for me) …
Thanks so much, Stephan
Hi @StephanPreibisch ,
thank you for the update!
I downloaded a vanilla Fiji (2023-07-20, win64), activated only the BigStitcher update site, and fused some of my data (1 angle, 3 channels, 1 illumination, 100 tiles, 1 timepoints, 0 missing views) to hdf5/xml using the N5-API.
I can confirm that:
So thats really fantastic :star_struck: !!
Opening the small demo dataset works seemingly fine, but when I open my own "big" h5/xml dataset (1 angle, 3 channels, 1 illumination, 100 tiles, 12 timepoints, 0 missing views, ~400 GB, registered but not fused, on Windows)
Plugins › BigDataViewer › Open XML/HDF5
) for the first time in a Fiji session is also slow, but the second time in the same Fiji session is fast as per usual.In older versions of BigStitcher/mvr/bdv (Using spimdata version: 0.9-revision, Using multiview-reconstruction version: 1.2.9, bdv jar6.2.2), this was much faster.
So somehow there seems to be a performance decrease to open/display the dataset, but I can't tell with certainty in which version of BigStitcher/mvr/bdv it was introduced.
Hi, is there any chance you can share this dataset with me? Then I could debug what is going on ... I do not have such delays ... maybe it's OS-related or it's the dataset.
Hi, I uploaded : T2_sect2_h5_tp0.zip (38.1 GB) : https://filesender.switch.ch/filesender2/?s=download&token=06cdbadb-406f-4e52-aafc-11175bac322a
I truncated the dataset (original: 1 angle, 3 channels, 1 illumination, 100 tiles, 12 timepoints, ~400 GB, registered but not fused) and included only timepoint 0, the other partitions are missing on purpose so the upload is smaller (38 GB). It still reproduces the delay-issue for me on Windows:
Great, thanks so much, will debug next week!
I just downloaded it and it opens in about 5-10 sec for me in my up-to-date Fiji … do you load it via a network connection maybe?
In any case I'll have a look what it does in these 10 secs ... might be revealing. Unfortunately, I have to do performance reviews this week, so only next week seems reasonable at this point
Hi @StephanPreibisch , thank you again for all the testing!
it opens in about 5-10 sec for me in my up-to-date Fiji … do you load it via a network connection maybe?
Thats a good point, I load indeed from network storage.
It is our common use case. In our facility we provide our user with 60+ virtual machines that all use a common network storage.
Plugins › BigDataViewer › Open XML/HDF5
), so maybe its a BDV issue rather than a BigStitcher issueThank you again for your help, its much appreciated :smiley:
@StephanPreibisch it seems that the delay is a BDV issue and has hence been moved to https://github.com/bigdataviewer/bigdataviewer-core/issues/165
Concerning BigStitcher, this then leaves only the last point
when closing the BigSitcher Window, the “select dataset for stitching explorer” Dialogue window opens again. It used not to be the case in previous versions.
that's actually on purpose :)
I found this much better, since often I do want to open another dataset ... if people hate it I am happy to add some sort of checkbox for it ...
that's actually on purpose :)
actually, after using it now for a couple of times, I liked it as well :)
issue description
When fusing a multi-resolution dataset (h5/xml) with the N5API to e.g. BDV-compatible HDF5, the resulting fused h5/xml only contains a single resolution level, see below screenshots from inspect both dataset in Fiji using
Plugins › HDF5 › Load HDF5 File...
potential downstream issues
Viewing "Big" fused image (e.g. > ~100 tiles) in BDV is terribly laggy / not feasible
reproduce the issue
download the demo dataset and run below IJ-macro code, then inspect both dataset in Fiji using
Plugins › HDF5 › Load HDF5 File...
Crosspost
https://forum.image.sc/t/bigstitcher-n5-api-fused-n5-hdf5-has-no-pyramids-and-does-not-display-well-in-bdv/80925