README.md

# synapsis

## Project overview

synapsis is an R package for analysing fluorescent microscopy images.

## Contributors

Lucy McNeill, St Vincent's Institute of Medical Research

Wayne Crismani, St Vincent's Institute of Medical Research and the University of Melbourne

## Compatibility

## Using synapsis

synapsis has four main functions. These are:

- auto_crop

- get_pachytene

- count_foci

- measure_distances

We summarise them in the following subsections:

### auto_crop

input: Original grey scale image files of (1) Synaptonemal complexes (e.g. SYCP3 anti-body) and (2) Foci (e.g. MLH1, MLH3 anti-body) channels from e.g. Nikon .nd2 files.

output: crops in channels (1) '*dna.jpeg' and (2) '*foci.jpeg' around individual cells.

![cropping](resources/figures/cropping_procedure.png)

### get_pachytene

input: crops in channels (1) '*dna.jpeg' and (2) '*foci.jpeg' around individual cells, from previous auto_crop.

output: only keeps crops if cells are in pachytene phase (based on channel (1))

### count_foci

input: crops of dna and foci channels in pachytene phase (from get_pachytene)

output: number of foci counts of synamtonemal complexes per cell (i.e. channel 1 coincident with channel 2) as a function of genotype.

### measure_distances

input:

output:

## Analysis

![cropping-hist](output/count_foci_histogram.png)

![cropping-box](output/count_foci_boxplot.png)

<img src="output/measure_distances_histogram.png" width="700" height="500">

<img src="output/measure_distances_boxplot.png" width="600" height="500">

## Project organisation and management

Please issue bug reports through GitLab.


## Acknowledgements

This project is a [workflowr][] project, where we make use of a [project template][] created by Davis McCarthy.

[workflowr]: https://github.com/jdblischak/workflowr

[project template]: https://gitlab.svi.edu.au/biocellgen-public/aaaa_2019_project-template