add contributing and clean readme

docs/CONTRIBUTING.md

+## Contributing
+
+We focus our work on python 3.7 due to the current neural network being developed on tensorflow 1. In the near future we will migrate the networ to pytorch to support more recent versions of all packages.
+
+### Issues
+All issues are managed within the gitlab [ repository ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/issues), if you don't have an account on the University of Edinburgh's gitlab instance and would like to submit issues please get in touch with [Prof. Peter Swain](mailto:peter.swain@ed.ac.uk ).
+
+### Branching
+* master: very sparingly and only for changes that need to be made in both
+ versions as I will be merging changes from master into the development
+ branches frequently
+ 
+Branching cheat-sheet:
+```git
+git branch my_branch # Create a new branch called branch_name from master
+git branch my_branch another_branch #Branch from another_branch, not master
+git checkout -b my_branch # Create my_branch and switch to it
+
+# Merge changes from master into your branch
+git pull #get any remote changes in master
+git checkout my_branch
+git merge master
+
+# Merge changes from your branch into another branch
+git checkout another_branch
+git merge my_branch #check the doc for --no-ff option, you might want to use it
+```
+
+### Data aggregation
+
+ALIBY has been tested by a few research groups, but we welcome new data sources for the models and pipeline to be as general as possible. Please get in touch with [ us ](mailto:peter.swain@ed.ac.uk ) if you are interested in testing it on your data.

docs/README.md

@@ -112,45 +112,6 @@ seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None,
                                 z=[0,1,2,3,4])
 ```
 
-## Reading MATLAB files
-*Disclaimer: this is very much still in development so it may not always
- work for you case. If you run into any problems please let me know, or even
- better start an Issue on the project describing your problem.*
-
-At the moment the best/only way to read matlab files is through a `matObject`:
-
-```python
-from aliby.io.matlab import matObject
-cTimelapse = matObject('/path/to/cTimelapse.mat')
-```
-
-You can see an overview of what's in the object:
-```python
-cTimelapse.describe()
-```
-
-The `matObject` has some dictionary-like features although it is *not* a
-dictionary (yet). You can access different parts of the object using keys
-, though, and can use the `keys()` function to do so. This will usually
-work at the first few levels, but if it doesn't you may have run into an
-object that's actually a list or a numpy array.
-
-```python
-cTimelapse.keys()
-```
-
-This should return an iterable of the upper level keys. For example, a
-timelapse object will usually have a `timelapseTrapsOmero` key which you
-can look deeper into in the same manner. Once you've found what you want
-you can usually access it as you would a nested dictionary, for instance:  
-
-```python
-cTimelapse['timelapseTrapsOmero']['cTimepoint']['trapLocations']
-```
-
-For more information about using MATLAB files in python objects, please see
- [this page](docs/matlab.md).
-
 ## Development guidelines
 In order to separate the python2, python3, and "currently working" versions 
 (\#socialdistancing) of the pipeline, please use the branches: