Nuclei Segmentation 3D (ImageJ)

Description

The macro will segment nuclei and separate clustered nuclei in a 3D image using a binary watershed. As a result an index-mask image is written for each input image.

need a thumbnail

Nuclei Segmentation 2D (ImageJ)

Description

The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask image is written for each input image.

need a thumbnail

InspectJ

Description

InspectJ is a free ImageJ/FIJI tool to inspect digital image integrity.

InspectJ_v2 is a newer version for advanced users. It applies additional features like histogram equalization and gamma correction for improved image inspections.

need a thumbnail

SpotDetectionIJ

Description

This is a classical workflow for spot detection or blob like structures (vesicules, melanosomes,...)

Step 1 Laplacian of Gaussian to enhance spots . Paraeters= radius, about the average spot radius

Step 2 Detect minima (using Find Maxima with light background option to get minima). Parameter : Tolerance to Noise: to be tested, hard to predict. About the height of the enhanced feautures peaks

has topic
has function
spot detection

Introduction to ImageJ macro language

Biologist
Microscopist

In this session, we will cover the basics of ImageJ macro programming using a simple example: how to quantify signal enrichment at the nuclear rim? Trainees will (re)discover how to record actions, plan a workflow and organise their code. This session will alternate presentation of technical points, to be directly applied during practical exercises. The macro will progressively complexify as new notions are taught.

2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.

Description

This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated). 

HyphaTracker

Description
HyphaTrackerWorkflow
HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.

hyphatracker

bleb dynamics

Description

The purpose of the workflow is ....

First you need

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NeuriteTracer

Description

"The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in two-dimensional fluorescence microscopy images of neuronal cultures. The plugin performed well on images from three different types of neurons with distinct morphologies."

This plugin requires parameter setting: Threshold levels and scale (see more details on the related publication)

Skin Tools

Description

The skin tools measure the thickness of the epidermis and the interdigitation index.

The input images are masks that represent the epidermis and that have been created from images of stained histological sections. The mask must touch the left and right border of the image. The dermal-epidermal border must be on the lower site of the image. The interdigitation index can be measured for one or more segments per image. As a measure of the thickness of the epidermis the lengths of a number of random line segments are measured. The line segments start at the lower border, are perpendicular to the lower border and end at the opposite border of the mask.

See installation Instructions on the website.

has topic
Measure thickness from a mask