spot detection

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FindFoci

Package/Library: 
Fiji
ImageJ
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MountainsMap

MountainsMap is a surface imaging and metrology software published by the company Digital Surf.
Its main application is micro-topography, the science of studying surface texture and form in 3D at the microscopic scale.
The software is used mainly with stylus-based or optical profilometers, optical microscopes and scanning probe microscopes.

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MicrobeTracker

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Centromere Recognition and Quantification

Workflow Language: 
ImageJ Macro Language
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Imaris

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

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Icy

Reproducing an experiment doesn’t stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team.

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Spot Detection

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