Volumetric 2P broken?

[CodyCBakerPhD]

https://neurosift.app/?p=/nwb&url=https://api.dandiarchive.org/api/assets/8477f3df-2feb-4da8-bb82-364f58a3a8ec/download/&dandisetId=000350&dandisetVersion=0.221219.1506&tab=neurodata-item:/acquisition/TwoPhotonSeries|TwoPhotonSeries

should show a whole brain zebrafish, but something seems quite off

Any ideas @magland?

[magland]

@CodyCBakerPhD This has now been fixed.

However, you will notice that it is slow to load every new frame. That's because it needs to load all the planes for every frame. The chunking should allow a much more efficient loading (see below), but neurosift does not right now have the ability to slice in this complex way. I guess that should be submitted as a separate issue.

In [1]: import lindi
   ...: 
   ...: url = 'https://lindi.neurosift.org/dandi/dandisets/000350/assets/8477f3df-2feb-4da8-bb82-364f58a3a8ec/zarr.json'
   ...: 
   ...: # Load the remote file
   ...: f = lindi.LindiH5pyFile.from_reference_file_system(url)
   ...: 
   ...: # load the neurodata object
   ...: X = f['/acquisition/TwoPhotonSeries']

In [2]: X
Out[2]: <LindiH5pyGroup: /acquisition/TwoPhotonSeries>

In [3]: X['data']
Out[3]: <LindiH5pyDataset: /acquisition/TwoPhotonSeries/data>

In [4]: X['data'].shape
Out[4]: (10050, 888, 2048, 30)

In [5]: X['data'].chunks
Out[5]: (1, 888, 2048, 1)

[CodyCBakerPhD]

Looks great, thanks