From 765392ddce1aeeee8c40991f9d2c26fe726d9da7 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 16:50:58 +0100
Subject: [PATCH 1/7] Update README.md

---
 README.md | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index dbded8a..df17de6 100644
--- a/README.md
+++ b/README.md
@@ -27,8 +27,9 @@ If you encounter any bugs or have suggestions for new features, please open an i
 
 Our package requires `python >= 3.9`.
 
+You can install the package directly from [PyPI](https://pypi.org/project/metaspace-converter/):
 ```bash
-pip install -U git+https://github.com/metaspace2020/metaspace-converter@master
+pip install metaspace-converter
 ```
 
 ### Import package
@@ -39,6 +40,8 @@ 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
 [python client](https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client)
 download datasets from METASPACE.
@@ -160,6 +163,11 @@ sdata.points["maldi_points"] = sdata.transform_element_to_coordinate_system(
 
 ![Image](docs/_static/img/example_img_sd.png)
 
+## License
+
+Unless specified otherwise in file headers or LICENSE files present in subdirectories, all files are licensed under the [Apache 2.0 license](https://github.com/metaspace2020/metaspace/blob/master/LICENSE).
+
+
 [badge-docs]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
 [badge-pypi]: https://img.shields.io/pypi/v/metaspace-converter
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests

From bb1fb9c584b1bf9a19cebf0e416137339dd124e8 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 16:55:39 +0100
Subject: [PATCH 2/7] Added anndata_to_image_array to examples.rst

---
 docs/examples.rst | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/docs/examples.rst b/docs/examples.rst
index c6b06af..6a8347c 100644
--- a/docs/examples.rst
+++ b/docs/examples.rst
@@ -51,6 +51,26 @@ SquidPy
 .. image:: ./_static/img/example_img_sq.png
    :alt: Visualization with SquidPy
 
+Convert AnnData objects to ion image arrays
+-------------------------------------------
+
+If you want to work with the ion images as numpy arrays, the function `anndata_to_image_array` can
+convert previously downloaded AnnData objects to numpy arrays.
+
+.. testcode::
+
+   from metaspace_converter import metaspace_to_anndata, anndata_to_image_array
+
+   # Download data
+   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
+   print(ion_images.shape)
+   # > (6, 61, 78)
+
+
 SpatialData
 -----------
 

From 75452e4aa95502844ee15e355cc38cd63f342da8 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 17:06:31 +0100
Subject: [PATCH 3/7] Added badges and installation instructions to docs index.

---
 docs/index.rst | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/docs/index.rst b/docs/index.rst
index cce353e..9449f5d 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,10 +6,23 @@
 Welcome to METASPACE Converter's documentation!
 ===============================================
 
+|Tests badge|
+|Docs badge|
+|PyPI badge|
+
 Functions to convert `METASPACE`_ datasets to `AnnData`_ objects.
 
 This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ ecosystem with METASPACE data.
 
+Installation
+------------
+You can install the package via pip:
+
+.. testcode::
+   
+   pip install metaspace-converter 
+
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
@@ -22,3 +35,11 @@ This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ eco
 .. _ScanPy: https://scanpy.readthedocs.io/en/stable/
 .. _SquidPy: https://squidpy.readthedocs.io/en/stable/
 .. _SpatialData: https://spatialdata.scverse.org/en/latest/
+
+
+.. |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
+.. |Docs badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
+    :target: https://metaspace2020.github.io/metaspace-converter/
+.. |PyPI badge| image:: https://img.shields.io/pypi/v/metaspace-converter
+    :target: https://pypi.org/project/metaspace-converter/

From b555f4eddd26787b58af4919df643cdaffc756fe Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 17:08:36 +0100
Subject: [PATCH 4/7] Updated authors

---
 docs/conf.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index ed364dd..ff16b8f 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -18,8 +18,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "METASPACE Converter"
-copyright = "2023, Tim Daniel Rose"
-author = "Tim Daniel Rose"
+copyright = "2023; Tim Daniel Rose, Andreas Eisenbarth, Theodore Alexandrov"
+author = "Tim Daniel Rose, Andreas Eisenbarth"
 
 
 # -- General configuration ---------------------------------------------------

From b1cc83e832a2b60d44a7eb7bc7680bd9d039a9c3 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 17:24:24 +0100
Subject: [PATCH 5/7] Testcode fix.

---
 docs/examples.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/examples.rst b/docs/examples.rst
index 6a8347c..f8423b4 100644
--- a/docs/examples.rst
+++ b/docs/examples.rst
@@ -70,6 +70,8 @@ convert previously downloaded AnnData objects to numpy arrays.
    print(ion_images.shape)
    # > (6, 61, 78)
 
+.. testoutput::
+   (20, 130, 143)
 
 SpatialData
 -----------

From 853181118dfcea5e054d7ccda8fb9755c2478c20 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 17:32:38 +0100
Subject: [PATCH 6/7] Update index.rst

---
 docs/index.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/index.rst b/docs/index.rst
index 9449f5d..599efc3 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -18,7 +18,8 @@ Installation
 ------------
 You can install the package via pip:
 
-.. testcode::
+
+.. code-block::
    
    pip install metaspace-converter 
 

From 114d68bf2b411f68b7569a9f1b77dc9ed31ecd17 Mon Sep 17 00:00:00 2001
From: Tim Daniel Rose <34072286+tdrose@users.noreply.github.com>
Date: Wed, 29 Nov 2023 17:33:15 +0100
Subject: [PATCH 7/7] Update examples.rst

---
 docs/examples.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/examples.rst b/docs/examples.rst
index f8423b4..4437811 100644
--- a/docs/examples.rst
+++ b/docs/examples.rst
@@ -68,9 +68,9 @@ convert previously downloaded AnnData objects to numpy arrays.
 
    # 6 ion images of shape 61x78
    print(ion_images.shape)
-   # > (6, 61, 78)
 
 .. testoutput::
+   
    (20, 130, 143)
 
 SpatialData