This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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
Detailed parameter description.
Usage
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 |
Usage
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 |