# Description
This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
 
# Automatic slice segmentation  

Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.


## How to setup the enviroment
### Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system

* 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/Linux is avaliable at  
  https://github.com/ANTsX/ANTs/releases/tag/v2.1.0

* Make sure to add 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 inserting
  ```sh
  export PATH=$PATH:usr/local/bin/ANTs:
  ```
  Here the path to the ANTs registration was $/usr/local/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.
  
  

* if permission denied, then the file needs to be made executable - this is done using the command
  ```sh
  chmod +x <...>/antsRegistration
  ```
  
* Make sure 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
  ```
  
  
## Prerequisites  
* A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.  
* A template file (.nii or .nii.gz)  
* A segmentation of the template file  (.nii or .nii.gz)  
  
## Usage  
* 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  
 
## Example.zip
In the repository is included a zip file that contains all the files and scripts
used in order to run an Example of the program. To run the example, download and
unzip the folder and open the folder in a terminal window. Make sure that the
enviroment is setup correct as descirbed above, and then run the shell fill by 
```sh
bash runner_example.sh
```


## Details
Detailed parameter description.

### runner.py
**Usage**
```sh  
python3 runner.py sliceloc segloc templateloc bregma [coord] outputdir
```  
In the subfolder 'Example' a shell script is provided that runs the programs as
intended with test brainslice.

**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 |
|`outputdir`| Location for the output of the registration files|
**Optional arguments**

| | |
|---|---|
|`--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  
python3 preprocess.py file dir -s Series --pdim [pixeldimensions]  
```  
**Positional/Required Arguments**

|||
|--------------------------------|-----------------------------|
|`file`            |Location of the file to be preprocessed (.tiff or .nd2) |
|`dir`            |Directory to output preprocessed files (will output .nii files)|
|`-s`|The series to extract (If input file is single-series, use 0 for this argument)|

**Optional arguments**

|||
|--------------------------------|-----------------------------|
|`--pdim [pixeldimensions]`            |Dimensions of pixels, if not provided, these will be extracted from image metadata|# Description
This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.