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
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
~/.bashrc
In the configfile add the path. This can be done by inserting
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
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
chmod +x <...>/antsRegistration
pip install nibabel
To check the version of a package
pip freeze | grep nibabel
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
bash runner_example.sh
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 |
This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.