ome-zarr-py

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Polygon and other vector data

3

Just adding an issue to keep track of the question I raised here: https://forum.image.sc/t/polygon-and-other-roi-annotations-in-ome-zarr/47990/9 According to the discussion above there does not seem to be a standard for storing polygon...

VolkerH

Add class annotations and/or other metadata properties to labels

16

Currently the labels spec supports the declaration of a `label-value` and its associated `color`. Commonly, label values have other associated information including the most obvious, the class name. napari also...

DragaDoncila

@jni pointed out that the multiscale information for 4007801 was missing. Only path "0" was listed. That has now been corrected, but one sanity check would be to detect if...

joshmoore

Update ome-zarr-py to display masks

4

Since napari reader can return a layer type, See https://napari.org/docs/plugins/hook_specifications.html#napari.plugins.hook_specifications.napari_get_reader we if this plugin can recognise a mask then it can be handled as a labels layer by napari. And...

joshmoore

Pipeline to generate ome-zarr format

4

I know the format is experimental, but are there available pipelines to generate the zarr format which adheres to the ome-metadata spec? I've tried `bioformats2raw`, which seems related, but I...

manzt

Memory usage can be improved by avoiding dtype conversions

1

I have noticed that the function `resize_image()` in `ome_zarr/scale.py` converts to dtype float, applies some downscaling and then converts back to the original dtype. This was the cause of poor...

LucaMarconato

ome_zarr download uses wrong dimension_separator

1

It seems that `ome_zarr download` is writing chunks with `"dimension_separator": "."`, even when downloading v0.4 data: ``` $ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0138A/TimEmbryos-102219/HybCycle_0/MMStack_Pos0.ome.zarr/ --output MMStack_Pos0.ome.zarr $ ls -al MMStack_Pos0.ome.zarr/0/ total 250256 drwxr-xr-x...

will-moore

Draft implementation of the new transform specs

6

@will-moore @joshmoore @bogovi @bogovicj (also please tag eventually missing relevant contributors). Giovanni (@giovp) and I have implemented a first draft of the [coordinate systems](https://github.com/scverse/spatialdata/blob/feature/transform_and_coord_spaces/spatialdata/_core/coordinate_system.py) and [coordinate transformations](https://github.com/scverse/spatialdata/blob/feature/transform_and_coord_spaces/spatialdata/_core/transform.py) in Python, in...

LucaMarconato

rgb_to_5d image code does not follow the spec

1

Hi all! According to the specification as a comment [here](https://github.com/ome/ome-zarr-py/blob/53d99c276ed8837b3e5384b92ecc352d15446284/ome_zarr/data.py#L87) the resulted array should be of shape `(t, c, z, y, x)`. Instead with `pixel.shape == 3` and `channels =...

ktsitsi

node.show() to render an Image with set_active_channels

1

This code provides a way to "set active channels" for a NGFF image, similar to omero-py [image.set_active_channels()](https://github.com/ome/omero-py/blob/7f979ce44b1fcbebfceb92cf51bf7c354a28ec57/src/omero/gateway/__init__.py#L8793) to render chosen channels with colours and min/max levels. Having written this code...

will-moore