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SpotFinderZ

Component
Description

Quote: *SpotFinderZ (from now on simply SpotFinder) detects round, usually diffraction-limited spots inside bacterial cells outlined with MicrobeTracker and places them into the meshes structure produced by MicrobeTracker. The program is written in MATLAB and saves the data in the MicrobeTracker format by appending additional fields.*

has topic
Bioimage informatics
has function
Object tracking
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PRIISM/IVE

Collection
Description

Priism is an image processing, analysis and visualisation application for multidimensional light and electron microscopy data. It uses the Image Visualization Environment (IVE) library, which is a closed-source C library with documented C and FORTRAN APIs. Priism/IVE was developed at UCSF, and can be obtained free of charge by sending an email request to the developers. Many of the same processing and analysis functions available in other image processing applications can be found here (cropping, resizing, spatial filters, Fourier transforms, segmentation etc.), and it includes a comprehensive html-based offline manual. The "SoftWoRx" package of GE Healthcare (formerly Applied Precision) was based on Priism/IVE.

Priism screenshot

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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DBSCAN clustering using PALMsiever

Workflow
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.

has topic
Single molecule localization microscopy
has function
Cell segmentation
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