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synapsis is an R package for analysing fluorescent microscopy images.
Lucy McNeill, St Vincent's Institute of Medical Research
Wayne Crismani, St Vincent's Institute of Medical Research and the University of Melbourne
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))
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
<img src="output/measure_distances_histogram.png" width="700" height="500">
- Boxplots
<img src="output/measure_distances_boxplot.png" width="550" height="500">
- Measures of statistical significance
with e.g. ANOVA testing.
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