Graph Plugin and Demo

Graph Plugin and Demo

Authors: Seth Berger (seth.berger at mssm.edu) and Dani Dumitriu (dani.dumitriu at mssm.edu)

History: 2012/03/20: First release

Source: Download vamp.zip, and uncompress to retrieve the source code.

Installation: Download vamp.zip and extraxt to a folder vamp in the "ImageJ" plugin folder.

Description:
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.

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Authors:	Seth Berger (seth.berger at mssm.edu) and Dani Dumitriu (dani.dumitriu at mssm.edu)
History:	2012/03/20: First release
Source:	Download vamp.zip, and uncompress to retrieve the source code.
Installation:	Download vamp.zip and extraxt to a folder vamp in the "ImageJ" plugin folder.
Description:	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.