[skip ci] DOC: Update citation in README.md and CITATION.cff

CITATION.cff

@@ -43,7 +43,7 @@ authors:
 - family-names: "Raza"
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
-title: "TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics"
+title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
 version: 1.2.1
 doi: 10.5281/zenodo.5802442
 date-released: 2022-07-07
@@ -93,8 +93,8 @@ preferred-citation:
   - family-names: "Raza"
     given-names: "Shan E Ahmed"
     orcid: "https://orcid.org/0000-0002-1097-1738"
-  doi: "10.1101/2021.12.23.474029"
-  journal: "bioRxiv"
-  month: 12
-  title: "TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics"
-  year: 2021
+  doi: "10.1038/s43856-022-00186-5"
+  journal: "Communications Medicine"
+  month: 09
+  title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
+  year: 2022

README.md

@@ -2,46 +2,69 @@
   <img src="https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/docs/tiatoolbox-logo.png">
 </p>
 <h1 align="center">TIA Toolbox</h1>
-<p align="center">
-  <a href="https://tia-toolbox.readthedocs.io/en/latest/?badge=latest">
-    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=latest" alt="Documentation Status" />
-  </a>
-  <a href="https://travis-ci.com/github/TissueImageAnalytics/tiatoolbox">
-    <img src="https://app.travis-ci.com/TissueImageAnalytics/tiatoolbox.svg?branch=master" alt="Travis CI Status" />
-  </a>
-    <a href="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox">
-      <img src="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox/branch/master/graph/badge.svg?token=7UZEMacQHm"/>
-    </a>
-    <a href="https://github.com/psf/black">
-      <img src="https://img.shields.io/badge/code%20style-black-000000.svg"/>
-    </a>
-    <a href="https://github.com/TissueImageAnalytics/tiatoolbox/tree/master#license">
-      <img src="https://img.shields.io/badge/license-BSD--3--clause-orange" />
-    </a>
-  <br>
-    <br>
   <a href="https://badge.fury.io/py/tiatoolbox">
     <img src="https://badge.fury.io/py/tiatoolbox.svg" alt="PyPI Status" />
   </a>
     <a href="https://pepy.tech/project/tiatoolbox">
-      <img src="https://static.pepy.tech/personalized-badge/tiatoolbox?period=total&units=international_system&left_color=grey&right_color=green&left_text=Downloads"/>
+      <img src="https://static.pepy.tech/personalized-badge/tiatoolbox?period=total&units=international_system&left_color=grey&right_color=green&left_text=downloads" alt="pypi Downloads"/>
     </a>
     <br>
     <a href="https://anaconda.org/conda-forge/tiatoolbox">
-      <img src="https://img.shields.io/conda/vn/conda-forge/tiatoolbox" />
+      <img src="https://img.shields.io/conda/vn/conda-forge/tiatoolbox"  alt="conda-forge badge"/>
     </a>
     <a href="https://anaconda.org/conda-forge/tiatoolbox">
-        <img src="https://anaconda.org/conda-forge/tiatoolbox/badges/downloads.svg" />
+            <img src="https://shields.io/conda/dn/conda-forge/tiatoolbox"  alt="conda-forge downloads"/>
     </a>
-
-<br>
-    <br>
-  <a href="https://doi.org/10.1101/2021.12.23.474029"><img src="https://img.shields.io/badge/bioRxiv-10.1101%2F2021.12.23.474029-blue" alt="DOI"></a>
-  <a href="https://zenodo.org/badge/latestdoi/267705904"><img src="https://zenodo.org/badge/267705904.svg" alt="DOI"></a>
-</p>
+  <br>
+  <a href="https://github.com/TissueImageAnalytics/tiatoolbox/tree/master#license">
+      <img src="https://img.shields.io/badge/license-BSD--3--clause-orange"  alt="License BSD-3-Clause"/>
+  </a>
+  <br>
+  <br>
+  <a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/pip-install.yml">
+    <img src="https://img.shields.io/pypi/pyversions/tiatoolbox.svg"  alt="Supported Python versions"/>
+  </a>
+ <a href="https://github.com/psf/black">
+      <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code Style black"/>
+    </a>
+  <a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml">
+    <img src="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml/badge.svg"  alt="GitHub Workflow passing"/>
+  </a>
+  <a href="https://tia-toolbox.readthedocs.io/en/latest/?badge=latest">
+    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=latest" alt="Documentation Status" />
+  </a>
+  <a href="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox">
+      <img src="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox/branch/master/graph/badge.svg?token=7UZEMacQHm" alt="Code Coverage"/>
+  </a>
+  <br><br>
+  <a href="https://doi.org/10.1038/s43856-022-00186-5"><img src="https://img.shields.io/badge/DOI-10.1038%2Fs43856--022--00186--5-blue" alt="DOI"></a>
 
 Computational Pathology Toolbox developed at the TIA Centre
 
+## Cite this repository
+
+If you find TIAToolbox useful or use it in your research, please consider citing our paper:
+
+Pocock, J. et al. TIAToolbox as an end-to-end library for advanced tissue image analytics. Communications Medicine 2, 120 (2022).
+
+```
+@article{
+    Pocock2022,
+    author = {Pocock, Johnathan and Graham, Simon and Vu, Quoc Dang and Jahanifar, Mostafa and Deshpande, Srijay and Hadjigeorghiou, Giorgos and Shephard, Adam and Bashir, Raja Muhammad Saad and Bilal, Mohsin and Lu, Wenqi and Epstein, David and Minhas, Fayyaz and Rajpoot, Nasir M and Raza, Shan E Ahmed},
+    doi = {10.1038/s43856-022-00186-5},
+    issn = {2730-664X},
+    journal = {Communications Medicine},
+    month = {sep},
+    number = {1},
+    pages = {120},
+    publisher = {Springer US},
+    title = {{TIAToolbox as an end-to-end library for advanced tissue image analytics}},
+    url = {https://www.nature.com/articles/s43856-022-00186-5},
+    volume = {2},
+    year = {2022}
+}
+```
+
 ## Getting Started
 
 ### All Users