Plant Image Analysis Plant Image Analysis

Endomembrane Quantifier

Robatzek lab @ Sainsbury Laboratory
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Scientific article
Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting.
M. Beck, J. Zhou, C. Faulkner, D. MacLean, S. Robatzek,
2012 , Plant Cell , 24(10), 4205
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High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis.
S. Salomon, D. Grunewald, K. Stüber, S. Schaaf, D. MacLean, P. Schulze-Lefert, S. Robatzek,
2010 , Plant Physiol. , 154(3), 1096
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EndomembraneQuantifier and EndomembranetCoLocQuantifier are two algorithms and software implementations for quantifying and identifying colocalized spot-like objects.

Images taken by high content and high-throughput confocal microscopy were analyzed with the image processing software Acapella (version 2.0; Perkin-Elmer). Based on an earlier developed algorithm referred to as the Endomembrane script, we designed an algorithm to robustly detect and quantify spots in one channel (GFP), which can subtract background autofluorescence signals in the same channel. In particular, spots were initially detected and then filtered based on their roundness, intensity, area, length, and width.

Additionally, EndomembraneCoLocQuantifier detects vesicles labeled with two different flourophores (e.g. GFP and RFP) and determines the amount of co-localization between these differentially labeled vesicles.

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Operating system


Measured variables
localisation, width, length, n-spots, shape,

Automation level

Plant requirements

Image requirements
microscopy, flex files,

Export formats

Other information
Require Acapella to run