5D or List< 4D >

[tischi]

@joshmoore

Citing @will-moore about opening ome.zarr in Napari

...since each image channel is split into a separate 4D layer, and then the labels are another 4D layer ...

I am doing the same for opening it in BDV as there the data model is List< 4D >.

This makes me wonder about the considerations that made you go for 5D rather than a list of 4D arrays (x,y,z,t)?!

I am not saying that I think List< 4D > is better, to me 5D feels quite natural and effective, I am just wondering!

[will-moore]

What we give napari is <5D array> & {channel_index: 2}, so napari does the slicing of the 5D array into channels (layers).

[tischi]

Just thinking out loud:

I have use cases where different channels should be displayed using a different transform in order to compensate for chromatic aberrations during the acquisition. For this I feel List< 4D > may be more natural, because every channel would have its own metadata such as the transform. However this could also be covered by channel specific metadata. One may also decide to just store different channels into different ome.zarr containers if they are "too different" from each other.

An advantage of 5D could be that one could downsample along the channel dimension in the resolution pyramids. I cannot think of a use case right now, but who knows, maybe for mass-spec imaging or other modalities with lots of channels this maybe be something useful at some point.

[jni]

Small note: in napari, I think passing in [4D arrays] and {channel_axis=0} probably works.

Having said that, I very much have a philosophical preference for a 5D array. I do think channel-specific metadata solves the chromatic aberration etc problems. For many image processing operations, it's easier to just have a 5D array than a list of arrays, at least in Python. e.g. background_intensity_over_time = np.percentile(im5d, 0.05, axis=(2, 3, 4)).

[tischi]

After the discussion yesterday in the NGFF meeting I wonder whether this issue could be closed and a new one should be opened in order to discuss the number of dimensions and axis labels in a broader sense?

Personally, I am happy to stick with 5D (XYZ, channel, time) for the time being.

[joshmoore]

a new one should be opened in order to discuss the number of dimensions and axis labels in a broader sense?

This makes sense from my POV, @tischi, but it may be good to leave this open until the other one exists ;)

[constantinpape]

I would second opening another more general discussion about dimension ordering and number of dimensions; this is also relevant for the transformation spec #28.

[constantinpape]

Ok, I went ahead and opened a new issue for the more general discussion, see #35.