Dendritic Spine

Spine Analyzer

Workflow
Description

Spine Analyzer allows to semi-automatically segment dendritic spines in 3D+t images and to measure their volumes and the intensities of the signal within in different channels over time.

has topic
Bioimage informatics
Digital histology
Microscopy
Fluorescence microscopy
has function
Interactive segmentation
Neurites with segmented dendritic spines

two-photon images of dendritic spines

Submitted by Perrine on Mon, 08/26/2019 - 11:35

Raw data of three types of dendritic spines imaged in biphoton (mushroom, tubby, thin spines).

Hippocampal neurons from mouse organotypic slice cultures 

 

If you use this dataset , please cite

M. U. Ghani, F. Mesadi, S. D. Kanik, A. O. Argunsah, A. Hobbiss, I. Israely, D. Unay, T. Tasdizen, and M. Cetin, "Shape and appearance features based dendritic spine classification," Journal of Neuroscience Methods.

Spine classification based on kernel density estimation

Component
Description

We propose to use a kernel density estimation (KDE) based approach for classification. This non-parametric approach intrinsically provides the likelihood of membership for each class in a principled manner. The implementation was used in Ghani2016. Any papers using this code should cite Ghani2016 accordingly. The software has been tested under Matlab R2013b.

 

Sample Data: Annotated two-photon images of dendritic spines

has function
Neuron image analysis
Classification
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