B6_dapi_template/README.md

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 '

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

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

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

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