gin commit from rMBP-15-Malthe.local

Modified files: 1

README.md

@@ -5,17 +5,45 @@ This repository contains the full data set for constructing the DAPI template, t
 
 Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
 
-## Dependecies
-* Python 3.7+
-* ANTs (https://github.com/ANTsX/ANTs) precompiled binaries
-  (https://github.com/ANTsX/ANTs/releases/tag/v2.1.0)
+## How to setup the enviroment
+* To run the program, Python 3.7+ is required. You can get the newest version of
+  python by installing Anaconda. To check the version of the python instalation
+  typing 
+  ````sh
+  python --version
+  ```
+* Install ANTs. This is done by adding a precompiled binaries to the libary
+  directory. The precompiled binaries for Mac/Win/Linux is avaliable at  
+  https://github.com/ANTsX/ANTs/releases/tag/v2.1.0
+
+* Make shure to ad ANTs to the path. This is done by editing the config file for
+  the terminal shell. The config file would often be named
+  ```sh
+  ~/.bashrc
+  ```
+  In the configfile add the path. This can be done by
+  ````sh
+  export PATH=$PATH:usr/lib/bin/ANTs:
+  ```
+  After adding this to the config file, restart the terminal and test if the
+  path was added correctly by typing
+  ````sh
+  which antsRegistration
+  ```
+  The correct path should then be printed.
+
+* Make shure to have installed or updated all packages listed in
+  requirements.txt. All the packages can be updated using pip. It is espicially
+  crucial to have installed to have installed the non standard packages Nibabel
+  and nipype. To install a a package i.e. Nibabel 
+  ````sh
+  pip install nibabel
+  ```
+  To check the version of a package 
+  ````sh 
+  pip freeze | grep nibabel
+  ```
 
-# Packages
-Make sure the following non-standard packages are installed:
-* Nipype
-* Nibabel
-
-If not already installed, you can use 'pip install <packagename> '
 
 ## Prerequisites  
 * A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.  
@@ -26,7 +54,6 @@ If not already installed, you can use 'pip install <packagename> '
 * Use runner.py to preprocess and output a sgementation registred to the slice
   in a designated output folder
 * Use preprocess.py to prepare input slice for automatic registration  
-* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.  
   
 ## Details
 Detailed parameter description.
@@ -54,28 +81,6 @@ intended with test brainslice.
 |---|---|
 |`--dapi [index]`   |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
 
-### auto_seg.py  
-**Usage**
-```sh  
-python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]  
-```  
-**Positional/Required Arguments**
-
-|||
-|--------------------------------|-----------------------------|
-|`sliceloc`            |Location of the slice you wish to register (.nii or.nii.gz) |
-|`segloc`            |Location of file containing segmentation of the template (.nii or.nii.gz)            |
-|`templateloc`|Location of template file (.nii or .nii.gz)|
-|`--bregma [coord]`|Bregma coordinate of input slice (if --approx argument is present, this is an optional argument)|
-
-**Optional arguments**
-
-| | |
-|---|---|
-|`--approx [index]`            |Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument.|
-|`--out [directory]`            |Provide an alternative output directory (default directory is /output)            |
-|`--dapi [index]`   |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
-
 ### preprocess.py  
 **Usage**
 ```sh