Skip to content

doc updates #113

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Nov 30, 2024
Merged

doc updates #113

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
d7d0876
BUG: Remove commented test code
thewtex Nov 30, 2024
56eb5d4
DOC: Update feature list
thewtex Nov 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 9 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,19 +8,23 @@

---

A lean and kind Open Microscopy Environment (OME) Next Generation File Format
(NGFF) Zarr implementation.
A lean and kind
[Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr](https://ngff.openmicroscopy.org)
implementation.

## ✨ Features

- Minimal dependencies
- Work with arbitrary Zarr store types
- Lazy, parallel, and web ready -- no local filesystem required
- Process extremely large datasets
- Conversion of most bioimaging file formats
- Multiple downscaling methods
- Supports Python>=3.8
- Implements version 0.4 of the
[OME-Zarr NGFF specification](https://github.com/ome/ngff)
- Supports Python>=3.9
- Reads OME-Zarr v0.1 to v0.5 into simple Python data classes with Dask arrays
- Optional OME-Zarr data model validation during reading
- Writes OME-Zarr v0.4 to v0.5
- Optional writing via [tensorstore](https://google.github.io/tensorstore/)

## Documentation

Expand Down
7 changes: 5 additions & 2 deletions docs/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,13 @@ A lean and kind
- Work with arbitrary Zarr store types
- Lazy, parallel, and web ready -- no local filesystem required
- Process extremely large datasets
- Conversion of most bioimaging file formats
- Multiple downscaling methods
- Supports Python>=3.9
- Implements version 0.4 of the
[OME-Zarr NGFF specification](https://github.com/ome/ngff)
- Reads OME-Zarr v0.1 to v0.5 into simple Python data classes with Dask arrays
- Optional OME-Zarr data model validation during reading
- Writes OME-Zarr v0.4 to v0.5
- Optional writing via [tensorstore](https://google.github.io/tensorstore/)

```{toctree}
:maxdepth: 2
Expand Down
24 changes: 0 additions & 24 deletions test/test_ngff_validation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,27 +69,3 @@ def test_validate_0_3():
def test_validate_0_3_no_version():
test_store = Path(__file__).parent / "data" / "input" / "v03" / "9528933.zarr"
from_ngff_zarr(test_store, validate=True)


# def test_z_y_x_valid_ngff():
# array = np.random.random((32, 32, 16))
# image = to_spatial_image(array)
# multiscale = to_multiscale(image, [2, 4])

# check_valid_ngff(multiscale)


# def test_z_y_x_c_valid_ngff():
# array = np.random.random((32, 32, 16, 3))
# image = to_spatial_image(array)
# multiscale = to_multiscale(image, [2, 4])

# check_valid_ngff(multiscale)


# def test_t_z_y_x_c_valid_ngff():
# array = np.random.random((2, 32, 32, 16, 3))
# image = to_spatial_image(array)
# multiscale = to_multiscale(image, [2, 4])

# check_valid_ngff(multiscale)
Loading