Step-by-step-installation-guide.md

+[[_TOC_]]
+
+## Before you start
+
 Installing and launching GEPARD requires a minimal knowledge of command line navigation. Everything you need can be found [here](Basics of command line navigation).
 
+
 ## Prepare Python environment
 
 ### Method 1 (recommended)
@@ -24,15 +29,16 @@ The compilation of tsp modules and running GEPARD will need to be performed in t
 We strongly advise against modifying this environment for any purpose as this could interfere with the functionality of GEPARD.
 
 
-
 ### Method 2 (not recommended)
-or
+
 Download Anaconda from https://www.anaconda.com/download. Choose the Python 3.8 version and follow the installer instructions. For help regarding installation, please refer to the Anaconda installation guide. Anaconda includes most of the required python libraries, however some packages need to be installed manually. To do that, start an Anaconda prompt from the Start Menu (Windows) or re-open a terminal (Linux, MacOS) and type the following:
 
 ```
 pip install opencv-python  
 conda install scikit-image dill cython
 ```
+
+
 ## Download Gepard
 
 Download the Gepard bundle from the repository at https://gitlab.ipfdd.de/GEPARD/gepard. Be careful to download the master branch, unless you know what you're doing:
@@ -41,6 +47,7 @@ Download the Gepard bundle from the repository at https://gitlab.ipfdd.de/GEPARD
 
 Extract all files into your preferred location. You should now have created a folder named `gepard-master`. Rename the folder to `gepard`.
 
+
 ## Build the tsp module
 
 The following step requires a C compiler. On Windows you will need to install Build Tools for Visual Studio. Most Linux distributions include GCC.
@@ -53,6 +60,7 @@ python setuptsp.py
 
 If a compiler is not available in your system, the command will produce an error. The exact wording depends on your operating system. 
 
+
 ## Start Gepard
 
 In the Anaconda prompt (Windows) or terminal (Linux, MacOS) navigate to the location containing the folder `gepard`. You can now start using Gepard in Simulated Raman Mode by typing:
@@ -60,9 +68,10 @@ In the Anaconda prompt (Windows) or terminal (Linux, MacOS) navigate to the loca
 python -m gepard
 ```
 
+
 ## Connect to a Raman microscope
 
-If you plan on using the WITec Raman interface to control your device, please note: **You use this interface at your OWN RISK!** 
+If you p## Table of contentslan on using the WITec Raman interface to control your device, please note: **You use this interface at your OWN RISK!** 
 
 Make sure that no obstacles block the objective and that you UNDERSTAND and VALIDATE the code that controls the microscope! Start with "witectesting.py", which should read and move within small margins.
 
@@ -81,6 +90,7 @@ To return to Simulated Raman Mode, set:
 raman_interface = SIMULATED_RAMAN_CONTROL
 ```
 
+
 ## Working with a different branch (advanced)
 
 - A newer –not yet released, but fairly stable– version of Gepard can be downloaded from branch ```Tiling2Develop```.  
@@ -119,6 +129,7 @@ conda install gcc_linux-64
 
 `ModuleNotFoundError: No module named 'Cython'` (Windows): Install or update Visual Studio Build Tools and try compiling again. 
 
+
 ## Errors related to Gepard operation
 
 `no module named gepard`: Please make sure that you are attempting to start Gepard from its parent folder, i.e. the location containing the folder "gepard".