Skip to content

Commit

Permalink
Fixed more Typos and removed Import section.
Browse files Browse the repository at this point in the history
  • Loading branch information
tdrose authored Nov 30, 2023
1 parent a2d27ec commit 73afe89
Showing 1 changed file with 8 additions and 14 deletions.
22 changes: 8 additions & 14 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ of many packages of the [scverse](https://doi.org/10.1038/s41587-023-01733-8) su
[squidpy](https://squidpy.readthedocs.io/en/stable/index.html) for spatial omics analysis.

Another supported format that is part of the [scverse](https://doi.org/10.1038/s41587-023-01733-8)
is [SpatialData](https://spatialdata.scverse.org/en/latest/) for storage, alignment, and processing
of spatial omics data. This enables users to easily align and integrate METASPACE datasets
is [SpatialData](https://spatialdata.scverse.org/en/latest/) for storing, aligning, and processing spatial omics data.
This enables users to easily align and integrate METASPACE datasets
to other spatial omics modalities.

If you encounter any bugs or have suggestions for new features, please open an issue in the
Expand All @@ -32,20 +32,14 @@ You can install the package directly from [PyPI](https://pypi.org/project/metasp
pip install metaspace-converter
```

### Import package

```python
import metaspace_converter
```

## Short tutorial

The full documentation for the package can be found here: [https://metaspace2020.github.io/metaspace-converter/](https://metaspace2020.github.io/metaspace-converter/)

The METASPACE-converter package is using the
The METASPACE-converter package uses the
[python client](https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client)
download datasets from METASPACE.
It serves as a wrapper that downloads converts datasets directly to
to download datasets from METASPACE.
It serves as a wrapper that downloads and converts datasets directly to
[AnnData](https://anndata.readthedocs.io/en/stable/index.html) and
[SpatialData](https://spatialdata.scverse.org/en/latest/) objects.

Expand Down Expand Up @@ -85,8 +79,8 @@ sc.pl.spatial(

#### Squidpy

Optical images can also be downloaded and save in the object if available.
Squidpy allows for an easy overlay of ion image and optical image.
Optical images can also be downloaded, if available, and saved in the object if available.

This comment has been minimized.

Copy link
@aeisenbarth

aeisenbarth Nov 30, 2023

Collaborator

The last "if available" is now too much.

I would also write "AnnData object" since the section doesn't yet mention what type of object.

Squidpy allows for an easy overlay of ion images and the optical image.

```python
from metaspace_converter import metaspace_to_anndata
Expand Down Expand Up @@ -130,7 +124,7 @@ print(ion_images.shape)
Download to the [SpatialData](https://spatialdata.scverse.org/en/latest/) format equally easy and
can be done with the `metaspace_to_spatialdata` function.

Here using a reversed colormap which better represents intense values on bright background.
Here using a reversed colormap which better represents intense values on a bright background.

```python
from metaspace_converter import metaspace_to_spatialdata
Expand Down

0 comments on commit 73afe89

Please sign in to comment.