Seth Berger (seth.berger at mssm.edu) and Dani Dumitriu (dani.dumitriu at mssm.edu)
2012/03/20: First release
and uncompress to retrieve the source code.
Download vamp.zip and extraxt to a folder vamp in the “ImageJ” plugin folder.
Vamp2D and Vamp 3D are connected threshhold growing tools for isolation of puncta in 2 and 3 dimensions. They are described in the paper “Vamping: New analytic tools yielding size and density measurements of PSD95 fluorescent
puncta highly correlated with electron microcopy quantification of postsynaptic densities” by Dumitriu et al. (Submitted to Journal of Neuroscience Methods, March 2012).
Abstract: The size of dendritic spines and postsynaptic densities (PSDs) is well-known to be correlated
with molecular and functional characteristics of the synapse as well as cognitive status. Thus, the
development of microscopy methods that allow high throughput quantification and measurement of
PSDs is a contemporary need in the field of neurobiology. While the gold standard for measurement of
sub-micrometer structures remains electron microscopy (EM), this method is exceedingly laborious
and therefore not always feasible. Immunohistochemistry (IHC) is a much faster technique for
identifying biological structures such as PSDs, but the fluorescent images resulting from it have
traditionally been harder to interpret. Here, we report on two new image analysis tools that result in
accurate size and density measurements of fluorescent puncta representing PSDs. The new technique
of vamping, using Volume Assisted Measurement of Puncta in 2 and 3 Dimensions (VAMP2D and
VAMP3D) respectively, was tested on the same subjects for whom we had previously obtained EM
measurements of PSD size and/or density. Based on highly consistent results between data obtained
by each of these methods, vamping offers an expedient alternative to EM that can nonetheless deliver a
high level of accuracy in measuring sub-cellular structures.
Author: Wayne Rasband (firstname.lastname@example.org) Date: 2000/8/28 Requirements: ImageJ 1.18s or later Source: SpecifyLine_.java Installation: Download SpecifyLine_.class to the plugins folder and restart ImageJ. Use the
Author: Wayne Rasband (email@example.com) History: 2000/11/28: First version 2003/01/28: Uses the image or selection min and max; works correctly with signed images Source: SixteenBit_Histogram.java Installation: