Hey @kevinyamauchi

I was trying to run your examples/save_load_points.py example, but ran into a missing matplotlib dependency. This should fix that dependency :)

hey @kevinyamauchi 👋

finally have time to try this out, although can't run example:

$ python examples/save_load_points.py
           y          x  size
0  47.642445  24.209154     3
1  80.593025  12.381161     3
2  83.739708  93.137802     3
3  17.738497  55.634464     3
4  58.593430  86.256935     3
5  32.610691  67.198502     3
6   9.933817  82.030869     3
7  75.796082  21.599758     3
8  12.506199  10.603416     3
9  82.929871  61.387028     3
/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
Traceback (most recent call last):
  File "/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_io/utils.py", line 214, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_io/specs/registry.py", line 175, in write_elem
    _REGISTRY.get_writer(dest_type, t, modifiers)(f, k, elem, *args, **kwargs)
  File "/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_io/specs/registry.py", line 64, in get_writer
    raise TypeError(
TypeError: No method has been defined for writing <class 'anndata._core.aligned_mapping.AxisArrays'> elements to <class 'zarr.hierarchy.Group'>

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "examples/save_load_points.py", line 32, in <module>
    write_points_dataset(
  File "/Users/giovanni.palla/Projects/ome-ngff-tables-prototype/src/ngff_tables_prototype/writer.py", line 106, in write_points_dataset
    write_table(points_group, points_anndata)
  File "/Users/giovanni.palla/Projects/ome-ngff-tables-prototype/src/ngff_tables_prototype/writer.py", line 38, in write_table
    write_attribute(group, "obsm", adata.obsm, dataset_kwargs)
  File "/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_io/utils.py", line 134, in write_attribute
    return write_elem(*args, **kwargs)
  File "/Users/giovanni.palla/miniconda3/envs/squidpy/lib/python3.8/site-packages/anndata/_io/utils.py", line 220, in func_wrapper
    raise type(e)(
TypeError: No method has been defined for writing <class 'anndata._core.aligned_mapping.AxisArrays'> elements to <class 'zarr.hierarchy.Group'>

Above error raised while writing key 'obsm' of <class 'zarr.hierarchy.Group'> to <zarr.storage.FSStore object at 0x7f9be6abf400>

do I maybe need a specific branch on ome-ngff ? I just cloned and installed so might be missing something

Thanks!

@jhnnsrs discovered that we were forcing the table keys to be lower case. This is incompatible with AnnData, which expects the dense matrix key to be X (i.e., upper case). This PR provides a fix by allowing the keys to be upper case when writting the AnnData group.

See discussion at https://github.com/ome/ngff/pull/64/files#r1025073730

In order to allow full access to all the tables metadata when the ability to ls subdirectories is not available (e.g. over https / s3), consolidate_metadata() can be used to add metadata to the image.zarr/tables group.

This would also provide a work-around for the listing of tables within that top-level tables group. See https://github.com/ome/ngff/pull/64/files#r1022858025

cc @ivirshup @joshmoore

Hi @kevinyamauchi !

Found potential typo in the reader.py This might be a quick fix for it? https://github.com/kevinyamauchi/ome-ngff-tables-prototype/pull/9 Lmk when do you think

I will keep playing with it. So far so good! 👍

Best, Tong

I'm trying to add an HCS example dataset, here's a WIP PR for this.

Motivation: Provide example data in the OME-NGFF High Content Screening format spec

My example dataset contains 2x2 field of views (fovs) for a single well, with label images, already saved in the OME-Zarr HCS spec. Additionally, I have feature measurements for each site saved as csvs and an example script that loads those measurements and saves them as an AnnData table per site. The saving seems to work nicely and I have an AnnData tables folder per fov. Really cool to see this working already!

Current issues:

1. I don't have a nice way to share example data. It's currently on a Google Drive, but my attempts to use gdown to download it from there directly have failed. Does anyone know an easy way to fix this? At the moment, one needs to follow the instructions in the example file to manually download the data first, unzip the OME-Zarr file & then run the example.
2. It seems the load_to_napari_viewer function is flipping x & y dimensions here. Is that intentional? When I open my images with the napari-ome-zarr plugin, they are displayed like this:

3. It appears the loading isn't designed to handle the plate spec. I haven't had time to look into it much. At the moment, I just load the first field of view, because load_to_napari_viewer throws a zarr.errors.ContainsGroupError: path 'tables' contains a group if I provide e.g. the full well (and full plates currently don't support displaying label images in ome-zarr-py, see here: https://github.com/ome/ome-zarr-py/issues/65#issuecomment-1155295470

Solved Issues:

1. I also used the library originally to save my label images to the OME-Zarr file. Saving 3D label images needed axes parameters & I added parsing for those for label images (not used in the example anymore, but maybe useful to somebody else)