Merge pull request #13 from metaspace2020/documentation-updates

Documentation updates

README.md

@@ -10,14 +10,14 @@ Datasets can be directly downloaded to
 [AnnData](https://anndata.readthedocs.io/en/stable/index.html) and
 [SpatialData](https://spatialdata.scverse.org/en/latest/) objects.
 
-[AnnData](https://anndata.readthedocs.io/en/stable/index.html) provides is underlying data format
+[AnnData](https://anndata.readthedocs.io/en/stable/index.html) is the underlying data format
 of many packages of the [scverse](https://doi.org/10.1038/s41587-023-01733-8) such as
 [scanpy](https://scanpy.readthedocs.io/en/stable/) for single-cell data analysis and
 [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
@@ -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.
 
@@ -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 AnnData object.
+Squidpy allows for an easy overlay of ion images and the optical image.
 
 ```python
 from metaspace_converter import metaspace_to_anndata
@@ -120,17 +114,17 @@ adata2 = metaspace_to_anndata(dataset_id="2023-11-14_21h58m39s", fdr=0.1)
 
 ion_images = anndata_to_image_array(adata2)
 
-# 6 ion images of shape 61x78
+# 20 ion images of shape 130x143
 print(ion_images.shape)
-# > (6, 61, 78)
+# > (20, 130, 143)
 ```
 
 ### SpatialData
 
 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

docs/examples.rst

@@ -66,7 +66,7 @@ convert previously downloaded AnnData objects to numpy arrays.
 
    ion_images = anndata_to_image_array(adata2)
 
-   # 6 ion images of shape 61x78
+   # 20 ion images of shape 130x143
    print(ion_images.shape)
 
 .. testoutput::

docs/index.rst

@@ -10,9 +10,26 @@ Welcome to METASPACE Converter's documentation!
 |Docs badge|
 |PyPI badge|
 
-Functions to convert `METASPACE`_ datasets to `AnnData`_ objects.
+Python package to download and convert datasets from the `METASPACE`_
+knowledge base to common formats for single-cell and spatial omics analysis.
+Datasets can be directly downloaded to
+`AnnData`_ and `SpatialData`_ objects.
+
+`AnnData`_ is the underlying data format
+of many packages of the `scverse`_ such as
+`ScanPy`_ for single-cell data analysis and
+`SquidPy`_ for spatial omics analysis.
+
+Another supported format that is part of the `scverse`_
+is `SpatialData`_ for storing, aligning, and processing spatial omics data. 
+This enables users to easily align and integrate METASPACE datasets to other spatial omics modalities.
+
+The METASPACE-converter package uses the `METASPACE python client`_
+to download datasets from METASPACE.
+If you also need to upload or modify datasets on METASPACE, please check the `Python client documentation`_.
+
+If you encounter bugs or have suggestions for new features, please open an issue on `GitHub`_.
 
-This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ ecosystem with METASPACE data.
 
 Installation
 ------------
@@ -31,12 +48,23 @@ You can install the package via pip:
    api
    examples
 
+License
+-------
+
+Unless specified otherwise source code in file headers or LICENSE files present in subdirectories, all files of this package are licensed under the `Apache 2.0 license`_.
+
+
+
 .. _METASPACE: https://metaspace2020.eu/
 .. _AnnData: https://anndata.readthedocs.io/en/stable/
 .. _ScanPy: https://scanpy.readthedocs.io/en/stable/
 .. _SquidPy: https://squidpy.readthedocs.io/en/stable/
 .. _SpatialData: https://spatialdata.scverse.org/en/latest/
-
+.. _scverse: https://doi.org/10.1038/s41587-023-01733-8
+.. _GitHub: https://github.com/metaspace2020/metaspace-converter
+.. _METASPACE python client: https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client
+.. _Python client documentation: https://metaspace2020.readthedocs.io/en/latest/index.html
+.. _Apache 2.0 license: https://github.com/metaspace2020/metaspace/blob/master/LICENSE
 
 .. |Tests badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests
     :target: https://github.com/metaspace2020/metaspace-converter/actions/workflows/tests.yml