hansenjn

MotiQ

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.

CiliaQ

An ImageJ plugin to quantify ciliary shape, length, and fluorescence.

SpermQ

An ImageJ plugin to analyze the flagellar beat of sperm, motile cilia beat, and sperm steering.

AdipoQ

A simple toolbox of ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.

MultifocalImaging-AnalysisToolbox

A toolbox to analyze spherical and filamentous objects in multifocal images with high precision.

ColorStackByTimeAndProject

ImageJ macros to color stacks by time point and create a video where the projection builds up frame by frame.

AdipoQ_Preparator

ImageJ plugin to quantify HE-staining images of adipose tissue.

SpermQ_Preparator

An ImageJ plugin to preprocess images for SpermQ analysis.

AdipoQ_Analyzer

ImageJ plugin to quantify HE-staining images of adipose tissue - Part II.

canny3d-thresholder

ImageJ plugin to preform image binarization based on a canny edge detection in 3 dimensions

CiliaQ_Editor

An ImageJ plugin to edit segmented channels in images output by CiliaQ_Preparator.

FreQ

An ImageJ plugin to analyze pixel intensity oscillations in time-lapse 2D images. For example, this allows to characterize the ciliary beat of multi-ciliated cells in time-lapse images acquired with a bright-field or phase-contrast microscope.

CiliaQ_Preparator

An ImageJ plugin to prepare images for analysis using CiliaQ.

ExtractSharpestPlane_JNH

ExtractSharpestPlane_JNH is an ImageJ/FIJI plugin to automatically extract the sharpest plane by highest SD from image stacks for large data sets.

imagej.github.io

The ImageJ wiki

list-of-update-sites

The update sites ImageJ2 knows about automatically

MultiFocal_AlignCurvesByLMS

A pure java tool to align bead profiles obtained by MultiFocalParticleTracker-Calibrator-3 across different planes by LMS.

MultiFocal_Preparation

An ImageJ plugin to convert raw camera recordings from a four-plane multifocal imaging setup, where the planes are projected to different positions of the camera chip, into a hyperstack (including image alignment and background and intensity corrections).

MultiFocalParticleTracker-Calibrator-3

An ImageJ plugin to obtain the width of beads in multifocal images for generating a calibration table.

MultiFocalParticleTracker-Complex-3

A plugin to calculate the z position of beads in multifocal images based on provding a calibrated relationship of bead radius and z position.

NuclQ

NuclQ - an ImageJ plugin to quantify intensity levels by distance to the nuclear membrane.

SpermQ-MF

Analyzing sperm in images from multifocal microscopy.

SpermQ-MF_GenerateLUT

By merging width recordings from piezo-driven multifocal z-stacks through immotile sperm, generate a Look-Up-Table for the relationship between the flagellar width and the flagellar z-position for different positions on the flagellum.

Tutorial

none

Volume_Viewer