# 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.

## Dependecies
* Python 3.7+
* ANTs (https://github.com/ANTsX/ANTs) precompiled binaries
  (https://github.com/ANTsX/ANTs/releases/tag/v2.1.0)

# 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.  
* 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  
* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.  
  
## 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|

### 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  
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|