Sc 40 issue cluster intensity (#78)

* SC_40 issue with coordinate system cluster intensity

* SC_40 update notebook

* SC_40 update flowsom clustering notebook

* SC_40 example with multiple coordinate systems for flowsom clustering

README.md

@@ -17,27 +17,27 @@ Note: This package is still under very active development.
 
 ## Installation
 
-Check out the docs for [installation instructions](docs/installation.md).
+Check out the docs for [installation instructions](https://github.com/saeyslab/harpy/blob/main/docs/installation.md).
 
 ## Tutorials
 
 Tutorials are available [here](https://harpy.readthedocs.io/en/latest/).
 
 ## Usage
 
-[Learn](docs/usage.md) how Harpy can be integrated into your workflow in different ways.
+[Learn](https://github.com/saeyslab/harpy/blob/main/docs/usage.md) how Harpy can be integrated into your workflow in different ways.
 
 ## Contributing
 
-See [here](docs/contributing.md) for info on how to contribute to Harpy.
+See [here](https://github.com/saeyslab/harpy/blob/main/docs/contributing.md) for info on how to contribute to Harpy.
 
 ## References
 
 - https://github.com/ashleve/lightning-hydra-template
 
 ## License
 
-Check license under license. Harpy is free for academic usage.
+Check the [license](https://github.com/saeyslab/harpy/blob/main/LICENSE). Harpy is free for academic usage.
 For commercial usage, please contact Saeyslab.
 
 ## Issues