Quantitation of ER Structure and Function

Abstract

The plant endoplasmic reticulum forms a network of tubules connected by three-way junctions or sheet-like cisternae. Although the network is three-dimensional, in many plant cells, it is constrained to a thin volume sandwiched between the vacuole and plasma membrane, effectively restricting it to a 2-D planar network. The structure of the network, and the morphology of the tubules and cisternae can be automatically extracted following intensity-independent edge-enhancement and various segmentation techniques to give an initial pixel-based skeleton, which is then converted to a graph representation. Collectively, this approach yields a wealth of quantitative metrics for ER structure and can be used to describe the effects of pharmacological treatments or genetic manipulation. The software is publicly available.

A systematic review and comparison of automated tools for quantification of fibrous networks

“…To quantify fibrin fiber diameter, we identified eight automated tools: DiameterJ 35 , Local Thickness plugin 36,37 , REAVER 38 , ER network analysis 39 , ACCMetrics 40,41 , CT-FIRE 24 , Quanfima 42 and SIMPoly 43 . Because a high image resolution is needed to quantify fibrin fiber diameters, we only tested these tools on STED and SEM images (Figure 3A).…”

“…We found seven different tools that quantify fiber length in confocal, STED, or SEM images: DiameterJ 35 , AngioTool 46 , REAVER 38 , ER network analysis 39 , CT-FIRE 24 , ACCMetrics 40,41 , and SOAX 47 (Figure 3C). The results of these tools showed strong correlations with each other when applied to STED and SEM images, but not for confocal images (Supplementary Tables VII-IX).…”

“…To automatically quantify the number of branch points, we found six tools: DiameterJ 35 , AngioTool 46 , StructuralGT 48 , REAVER 38 , ER network analysis 39 , and ACCMetrics 40,41 . Again, strong correlations were found between the results of the tools in both SEM and STED images, with remarkably higher absolute numbers of branch points per μm 2 in SEM than in STED or confocal images (Figure 3D and Supplementary Tables XI-XIII).…”

“…SIMPoly is a MATLAB-based tool that is very user-friendly 43 . The ER network analysis tool provides more user control because it has many options that can be adjusted, but it therefore requires more testing by the user for their specific images 39 .…”