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This is the development version of synapsis; for the stable release version, see synapsis.

An R package to automate the analysis of double-strand break repair during meiosis

Bioconductor version: Development (3.20)

Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.

Author: Lucy McNeill [aut, cre, cph] , Wayne Crismani [rev, ctb]

Maintainer: Lucy McNeill <luc.mcneill at>

Citation (from within R, enter citation("synapsis")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using-synapsis HTML R Script
Reference Manual PDF


biocViews SingleCell, Software
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports EBImage, stats, utils, graphics
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Suggests knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package synapsis_1.11.0.tar.gz
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macOS Binary (x86_64) synapsis_1.11.0.tgz
macOS Binary (arm64) synapsis_1.11.0.tgz
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