Automated

MountainsMap

Collection
Description
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. MountainsMap is mainly offered as embedded or optional OEM analysis software by most profilometer and microscope manufacturers, usually under their respective brands; it is sold for instance as: MountainsMap - X on Nikon's microscopes Leica Map on Leica's microscopes ConfoMap on Carl Zeiss' microscopes
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idTracker: Tracking animals

Component
Description

idTracker is a videotracking software that keeps the correct identity of each individual during the whole video. It works for many animal species including mice, insects (Drosophila, ants) and fish (zebrafish, medaka, stickleback). idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. Technique details and analyses of several applications are described in Pérez-Escudero et al (2014).

Video protocol: https://www.youtube.com/watch?v=oC9tp5TKAyw

Example image: Example video of 5 zebrafish

has function
Object tracking

3D affine transformation based on paired points

Component
Description

Using a text file containing 3D point coordinates as reference pairs, 3D image stack is transformed.

has function
Affine transformation
Linear transformation

Tracing data using PALMsiever

Workflow
Description
Tracer allows the user to create a trace along a structure in an image. It uses the underlying molecule positions, not the rendered image.
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Generate animations from image data

Workflow
Description
Imaris is a commercial 3D image visualisation and analysis tool. It can be used to produce complex 3D animations that include multiple volume and surface elements in several channels, as well as clipping planes and annotations such as text and arrows. Movies interpolate seamlessly between user-defined key frames, and properties such as viewing angle, zoom and visibility of each element can be changed during the animation. These features allow effective communication of results based on image data.
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