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Analysis toolbox for multifocal images

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@hansenjn hansenjn released this 01 Jul 07:19
· 2 commits to master since this release
v1.0.0
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The toolbox for analysis of multifocal images contains a collection of ImageJ plugins, java tools, and Matlab scripts to analyze spherical and filamentous objects in 3D with high speed and high precision based on multifocal images.

This release collects all tools required to use the toolbox at this point. For details on how to use the collection of tools see the User Guide, Example Data, and Matlab Scripts. In this release, we deposited copies of the executable .jar files for the ImageJ plugins or java-based tools to allow a direct application of the toolbox based on this release. To access source code for the individual ImageJ plugins or java-based tools, visit the respective release pages linked below.

Included tools

  • Multifocal_Preparation Release v0.0.1: An ImageJ plugin to convert raw multifocal recordings into a hyperstack (including image alignment and background and intensity corrections).
  • MultiFocalParticleTracker-Calibrator-3 Release v0.0.2: An ImageJ plugin to obtain the width of beads at different heights from multifocal images to generate a calibration table.
  • MultiFocal_AlignCurvesByLMS Release v0.0.1: A java tool to align bead profiles obtained by MultiFocalParticleTracker-Calibrator-3 across different planes by calculating the Least Mean Square (LMS) of the variance.
  • MultiFocalParticleTracker-Complex-3 Release v0.1.1: An ImageJ plugin to calculate the z position of beads from multifocal images based on a calibrated relationship of bead radius and z position.
  • SpermQ-MF Release v0.3.2: An ImageJ plugin for analyzing flagella/filaments in images from multifocal microscopy.
  • SpermQ-MF_GenerateLUT Release v0.1.0: By merging width recordings from piezo-driven multifocal z-stacks through immotile sperm, obtained with SpermQ-MF, this plugin generates a Look-Up-Table between the flagellar width and the flagellar z-position at different positions along the flagellum.
  • Matlab scripts to explore the output files from the ImageJ plugins 'MultiFocalParticleTracker-Complex-3' and 'SpermQ-MF' are contained in this repository and provided with this release.
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