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+ # Description
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+This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
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+
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+# Automatic slice segmentation
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+
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+Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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+
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+
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+## Dependencies
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+* Python 3.6
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+* Ants (https://github.com/ANTsX/ANTs)
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+* Various python packages detailed in requirements.txt
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+
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+## Prerequisites
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+* A high-resolution, DAPI modality TIFF image of a brain slice. Can have multiple channels.
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+* A template file (.nii or .nii.gz)
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+* A segmentation of the template file (.nii or .nii.gz)
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+
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+## Usage
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+* Use preprocess.py to prepare input slice for automatic registration
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+* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.
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+
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+## auto_seg.py
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+**Usage**
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+```sh
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+python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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+```
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+**Positional/Required Arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`sliceloc` |Location of the slice you wish to register (.nii or.nii.gz) |
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+|`segloc` |Location of file containing segmentation of the template (.nii or.nii.gz) |
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+|`templateloc`|Location of template file (.nii or .nii.gz)|
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+|`--bregma [coord]`|Bregma coordinate of input slice (if --approx argument is present, this is an optional argument)|
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+
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+**Optional arguments**
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+
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+| | |
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+|---|---|
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+|`--approx [index]` |Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument.|
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+|`--out [directory]` |Provide an alternative output directory (default directory is /output) |
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+|`--dapi [index]` |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
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+
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+## preprocess.py
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+**Usage**
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+```sh
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+python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
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+```
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+**Positional/Required Arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`file` |Location of the file to be preprocessed (.tiff or .nd2) |
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+|`dir` |Directory to output preprocessed files (will output .nii files)|
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+|`-s`|The series to extract (If input file is single-series, use 0 for this argument)|
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+
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+**Optional arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`--b [True/False]` |Bias field correction: Whether to use bias-field correction in preprocessing (default: True)|
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+|`--pdim [pixeldimensions]` |Dimensions of pixels, if not provided, these will be extracted from image metadata|
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+
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