Computational protocol: Dendritic morphology, synaptic transmission, and activity of mature granule cells born following pilocarpine-induced status epilepticus in the rat

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Protocol publication

[…] The complexity of dendritic trees in newborn granule cells labeled by GFP was quantitated by Sholl analysis. Sections of 80 μm in thickness were prepared and the GFP signals were immunofluorescently amplified to prevent rapid bleaching as described above. Z-series stack of 2 μm thick was taken in GFP-positive cells locating in the suprapyramidal blade with a 20X objective (zoom = 1). For each rat, 3 to 4 cells were scanned. Only neurons displaying intact dendritic arborization were analyzed. After GFP-positive soma and apical dendrites were traced under ImageJ ( with the NeuronJ plugin (, Sholl analysis was carried out by using ImageJ with the “Sholl analysis” plugin. The interval between concentric circles was 25 μm with the center point at the soma. […]

Pipeline specifications

Software tools Sholl analysis, ImageJ, NeuronJ
Application Microscopic phenotype analysis
Organisms Rattus norvegicus
Diseases Epilepsy
Chemicals Pentylenetetrazole, Pilocarpine