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Sholl analysis specifications


Unique identifier OMICS_25766
Name Sholl analysis
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 3.6.12
Stability Stable
Maintained Yes


No version available


  • person_outline Tiago Ferreira

Publication for Sholl analysis

Sholl analysis citations


Absence of Wdr13 Gene Predisposes Mice to Mild Social Isolation – Chronic Stress, Leading to Depression Like Phenotype Associated With Differential Expression of Synaptic Proteins

PMCID: 5930177
PMID: 29743870
DOI: 10.3389/fnmol.2018.00133
call_split See protocol

[…] mice were studied. A minimum of six CA1 neurons from 3-5 hippocampal sections for each mouse () were analyzed for dendritic branching. CA1 neurons were selected as described in previous reports (; ). Sholl analysis was carried out using NeuronJ plugin and Sholl Analysis plugin (v1.0) of ImageJ software. […]


GABAergic inhibition in dual transmission cholinergic and GABAergic striatal interneurons is abolished in Parkinson disease

Nat Commun
PMCID: 5897332
PMID: 29651049
DOI: 10.1038/s41467-018-03802-y

[…] s, as well as morphological metric measurements were performed using the semi-automated “Simple Neurite Tracer” plugin ( Based on dendrites reconstructions, a Sholl analysis was performed using “Sholl Analysis” plugin ( […]


Layer 5 Callosal Parvalbumin Expressing Neurons: A Distinct Functional Group of GABAergic Neurons

PMCID: 5845545
PMID: 29559891
DOI: 10.3389/fncel.2018.00053

[…] ally reconstructed in three dimensions using the Simple Neurite Tracer plugin for ImageJ. Cell morphological measurements, including calculation of soma area, dendritic length, number of branches and Sholl analysis (Sholl, ), were performed using the Simple Neurite Tracer plugin (Longair et al., ; Ferreira et al., ) and region of interest measurement tool in ImageJ. […]


Caffeine and Modafinil Ameliorate the Neuroinflammation and Anxious Behavior in Rats during Sleep Deprivation by Inhibiting the Microglia Activation

PMCID: 5863523
PMID: 29599709
DOI: 10.3389/fncel.2018.00049
call_split See protocol

[…] e immune-stained sections were observed under Olympus (Melville, NY, USA) BX51TF microscope and images were taken from the DG, CA1 and CA3 regions of the dorsal hippocampus of the brain. We performed sholl analysis for the morphological evaluation of astrocytes and microglial cells. The cell quantification was performed using stereo investigator program. Similarly, immunoreactivity of astrocytes a […]


Implantation of Neuronal Stem Cells Enhances Object Recognition without Increasing Neurogenesis after Lateral Fluid Percussion Injury in Mice

PMCID: 5818962
PMID: 29531536
DOI: 10.1155/2018/4209821
call_split See protocol

[…] analysis. Per animal, the five most mature-appearing cells with complete dendritic trees within the section were chosen for analysis. Dendritic length and branching pattern were calculated using the Sholl analysis plugin algorithm for ImageJ/Fiji [–]. […]


The Differentiation of Rat Oligodendroglial Cells Is Highly Influenced by the Oxygen Tension: In Vitro Model Mimicking Physiologically Normoxic Conditions

Int J Mol Sci
PMCID: 5855553
PMID: 29364139
DOI: 10.3390/ijms19020331
call_split See protocol

[…] The complexity of the elaborated oligodendroglial processes was estimated by means of the ImageJ software allowing for Sholl analysis (Sholl Analysis vs. 3.7.0, available online: [,]. The most representative CNP-stained cells cultured either under 5% or 21% oxygen were chosen for a subsequent […]


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Sholl analysis institution(s)
Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada; Department of Neuroscience, Physiology, and Pharmacology, University College London, London, UK; McGill Integrated Program in Neuroscience, Montreal, QC, Canada; Department of Biology, McGill University, Montreal, QC, Canada
Sholl analysis funding source(s)
Supported by the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation and the UK Medical Research Council.

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