Automated

Description

DBSCAN (Density-based spatial clustering of applications with noise) performs multi-dimensional clustering based on the local density of points. This plugin is implemented for 2-3 dimensions.

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Description

Two workflows are proposed here:

one based on fiducials, the other one on cross-correlation.

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Description
Sieving (or filtering) is choosing the good localizations and discarding the false ones. This operation is performed by inspecting the distribution of the localizations' fitted parameters and changing the min and max accordingly.
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Description

A clear tutorial on how to write a MATLAB script to segment clustered cells.

The full script is downloadable near the bottom of the article. 

Description

Matlab toolbox to analyze single molecule mRNA FISH data. Allows counting the number of mature and nascent transcripts in 3D images. See 2513. Following toolboxes are required: - Optimization toolbox - Statistics toolbox - Image processing toolbox - (Optional) Parallel processing toolbox

 

Input data type: 3D image

Output data type: CSV

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