Pixel-based colocalisation

Synonyms
Voxel-based colocalisation
Pixel-based colocalization
Pixel-based co-localisation
Manders coefficient

SODA suite

Component
Description

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

has topic
Bioimage informatics
Confocal fluorescence microscopy
Super-resolution microscopy
has function
Colocalisation analysis
Pixel-based colocalisation
Icy SODA logo

Aivia - Aivia Cloud - Aivia Web

Collection
Workflow
has topic
Machine learning
has function
Analysis
Frequency analysis
Image analysis
Colocalisation analysis
Object-based colocalisation
Pixel-based colocalisation
Filament tracing
Image feature detection
Image segmentation
Cell segmentation
Pixel classification
Neuron image analysis
Object classification
Object counting
Texture extraction
Object tracking
Cell tracking
Particle tracking
Annotation
Classification
Editing
Image deconvolution
Visualisation
Image visualisation
Volume rendering
Plotting

CEM

Collection
Description

Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

CEM runs as an imageJ plugin with an optional Matlab extension to remove cell bodies. More details are published at Kerman et al. 2015 Development. Supplemental Material includes a detailed user manual and the download link.

has topic
High content screening
has function
Neuron image analysis
Dilation
Pixel-based colocalisation
Image feature detection
Colocalisation analysis
Myelin

JACoP

Component
Description

This ImageJ plug-in is a compilation of co-localization tools. It allows:

-Calculating a set of commonly used co-localization indicators:

Pearson's coefficient Overlap coefficient k1 & k2 coefficients Manders' coefficient Generating commonly used visualizations:

-Cytofluorogram

Having access to more recently published methods:

-Costes' automatic threshold

Li's ICA Costes' randomization Objects based methods (2 methods: distances between centres and centre-particle coincidence)

has topic
Fluorescence microscopy
has function
Object-based colocalisation
Object-based colocalisation
Pixel-based colocalisation
Colocalisation analysis
Colocalisation analysis
example of partial colocalisation from reference publication
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