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.

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

Once we have the foci counts (count_foci) and/or distance between foci along synaptonemal complexes (measure_distances), we can generate

• Histograms

• Boxplots

• Measures of statistical significance

with e.g. ANOVA testing.

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.