Vesicles Data

Point pattern of synaptic vesicles observed in rat brain tissue.

datasets, spatial

As part of a study on the effects of stress on brain function, Khanmohammadi et al (2014) analysed the spatial pattern of synaptic vesicles in 45-nanometre-thick sections of rat brain tissue visualised in transmission electron microscopy. To investigate the influence of stress, Khanmohammadi et al (2014) study the distribution of the synaptic vesicles in the pre-synaptic neuron in relation to the active zone of the presynaptic membrane. They hypothesize that the synaptic vesicle density is a decreasing function of distance to the active zone.

The boundaries for the active zone, mitochondria, pre- and post synaptic terminals, and the centre of the synaptic vesicles were annotated by hand on the image.


The dataset vesicles is a point pattern (object of class "ppp") representing the location of the synaptic vesicles. The window of the point pattern represents the region of presynapse where synaptic vesicles were observed in this study. There is a hole in the window, representing the region occupied by mitochondria, where synaptic vesicles do not occur.

The dataset vesicles.extra is a list with entries ll{ presynapse outer polygonal boundary of presynapse mitochondria polygonal boundary of mitochondria mask binary mask representation of vesicles window activezone line segment pattern representing the active zone. } All coordinates are in nanometres (nm).

Raw Data

For demonstration and training purposes, the raw data files for this dataset are also provided in the spatstat package installation: ll{ vesicles.txt spatial locations of vesicles presynapse.txt vertices of presynapse mitochondria.txt vertices of mitochondria vesiclesimage.tif greyscale microscope image vesiclesmask.tif binary image of mask activezone.txt coordinates of activezone } The files are in the folder rawdata/vesicles in the spatstat installation directory. The precise location of the files can be obtained using system.file, as shown in the examples.


Nicoletta Nava, Mahdieh Khanmohammadi and Jens Randel Nyengaard. Experiment performed by Nicoletta Nava at the Stereology and Electron Microscopy Laboratory, Aarhus University, Denmark. Images were annotated by Mahdieh Khanmohammadi at the Department of Computer Science, University of Copenhagen. Jens Randel Nyengaard provided supervision and guidance, and curated the data.


Khanmohammadi, M., Waagepetersen, R., Nava, N., Nyengaard, J.R. and Sporring, J. (2014) Analysing the distribution of synaptic vesicles using a spatial point process model. 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, Newport Beach, CA, USA, September 2014.

  • vesicles
  • vesicles.extra
     plot(activezone, add=TRUE, col="red"))

## read coordinates of vesicles from raw data, for training purposes
vf <- system.file("rawdata/vesicles/vesicles.txt", package="spatstat")
vdf <- read.table(vf, header=TRUE)
Documentation reproduced from package spatstat, version 1.41-1, License: GPL (>= 2)

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