GitBook: [master] 2 pages modified

Author: ablot

README.md

@@ -28,11 +28,13 @@ For detailed instructions see [Installation](installation/installation.md)
 
 ## Usage
 
+To run the cell detection just do: 
+
 ```text
 cellfinder -s signal_channel_images  optional_signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5
 ```
 
 {% hint style="info" %}
-For more information see [Getting started](user-guide/getting-started.md)
+For more information and other options or analysis see [Getting started](user-guide/getting-started.md)
 {% endhint %}
 

user-guide/getting-started.md

@@ -15,19 +15,19 @@ Make sure you activate your conda environment before running cellfinder
 
 ### Running cellfinder
 
-cellfinder can be run with a single terminal command \(`cellfinder`\):
+The cell detection via cellfinder can be run with a single terminal command \(`cellfinder`\):
 
 ```text
     cellfinder -s signal_channel_images  -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5
 ```
 
-Multiple channels can also be processed at once with the same registration: 
+Multiple channels can also be processed at once: 
 
 ```text
 cellfinder -s first_signal_channel_images  second_signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5
 ```
 
-However, there are many options to change what parts of the analysis are run, and how they are run. I recommend looking through the [Command line options](usage/).
+However, there are many options to change what parts of the analysis are run, and how they are run. For instance, to register the brain to the allen reference atlas, use `--register`. I recommend looking through the [Command line options](usage/).
 
 {% hint style="warning" %}
 If you have any spaces in your file-path, please enclose it in quotation marks, otherwise cellfinder will interpret it as two inputs, separated by a space.