Semiautomated Analysis of Dendrite Morphology in Cell Culture

Abstract

Quantifying dendrite morphology is a method for determining the effect of biochemical pathways and extracellular agents on neuronal development and differentiation. Quantification can be performed using Sholl analysis, dendrite counting, and length quantification. These procedures can be performed on dendrite-forming cell lines or primary neurons grown in culture. In this protocol, we describe the use of a set of computer programs to assist in quantifying many aspects of dendrite morphology, including changes in total and localized arbor complexity.

Long noncoding RNA GM12371 acts as a transcriptional regulator of synapse function

“…Because we observed a major change in spine morphology with GM12371 knockdown, we asked whether GM12371 expression might be critical for dendritic tree complexity. As described in the spine analysis experiments above, hippocampal neurons were transfected with pEGFPN1 to visualize neuronal architecture and confocal projection images of dendritic arbors were collected for Sholl analysis ( 46 ). Intriguingly, GM12371 knockdown produced a significant reduction in dendritic tree complexity ( Fig.…”

A Novel Short Isoform of Cytosolic PSD-95 Interactor (Cypin) Regulates Neuronal Development

“…4), we asked whether cypinS regulates dendrite branching. Cypin and cypinS were overexpressed on DIV7 in cultured rat hippocampal neurons, and dendrite branching was analyzed at DIV12 using Sholl analysis [15–17]. It is important to note that cypinS is not expressed in rat neurons [2,3,7,8], and thus, we used these neurons to determine the role for cypinS in a null background.…”

“…All images were analyzed using ImageJ software (NIH) and MATLAB (MathWorks). Sholl analysis was performed using the Bonfire program developed by the Firestein laboratory [15–17]. In brief, concentric circles were drawn around the soma every 6 μm and intersections with dendrite branches were counted.…”

Overexpression of cypin alters dendrite morphology, single neuron activity, and network properties via distinct mechanisms

“…Semi-automated Sholl analysis was performed as described previously [12][13][14][15]. Briefly, images of hippocampal neurons were traced using the NeuronJ plugin for ImageJ (NIH).…”