Nuclei Tracking (ImageJ)

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Spot Detection 3D (ImageJ)

Description

This workflow detects spots from a 3D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the Threshold  value s input.

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Spot detection (ImageJ)

Description

This workflow detects spots from a 2D image by using straightforward set of ImageJ components. It receives the Laplacian Radius and the Noise tolerance as input.

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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.

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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

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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).