Affine + Consistent Elastic 2D Image Registration

2009-03-11T12:45:42+02:00

This macro aligns a stack of images taking the first image as reference in two steps: MOPS and bUnwarpJ. The parameters from both methods are introduced in a common dialog. Requirements You need to have previously installed the plugins SIFT/MOPS from Stephan Saalfeld and bUnwarpJ from Ignacio Arganda-Carreras.

Auto Correlation

2008-10-24T11:49:06+02:00

A macro to determine image focal quality image-wide (not ROI-wide) // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-12 "AutoCorrelation" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.1 // Date: 14/07/2006 // Author: Andy Weller macro "Auto_Correlation" { W = getWidth(); H = getHeight(); b = 0; c = 0; autoCorr = 0; // Set to 0 which is out of focus for (j=0; j

Brenner Gradient

2010-01-27T13:16:23+02:00

A macro to determine image focal quality image-wide (not ROI-wide) // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-3 "Brenner Gradient" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.1 // Date: 14/07/2006 // Author: Andy Weller macro "Brenner_Gradient" { W = getWidth(); H = getHeight(); brenner = 0; // Set to 0 which is out of focus for (j=0; j

Distribution Plotter

2009-12-02T06:05:45+02:00

Plots frequencies on a double Y-axis graph from a selected column of the Results Table. [Distribution Plotter Screenshot] Tiago Ferreira, 2009.11.19 ---------- Code: // This macro plots cumulative and relative frequencies using values from the // Results table. Cumulative frequencies are displayed on the left Y axis while // relative frequencies are plotted on the right Y axis. To increase readability, // height of modal class is matched to the 50th-percentile. // TF - 2009.11.10 // Unco…

GFP-LC3

2009-06-02T04:25:21+02:00

GFP-LC3 Introduction Microtubule associated protein light chain 3(LC3) is a ubiquitin-like protein that binds to autophagosomes (AVs). Cellular biologists transfect mammalian cells with GFP tagged LC3 to track and follow the fate of AVs in the cell and to measure autophagic flux.

Import Zeiss lookup tables

2010-03-29T16:41:07+02:00

This macro imports a Zeiss lookuptable file, as found in the AIM or ZEN software, and applies it to the current image. // This macro imports a Zeiss lookuptable file, as found in the AIM or ZEN software. // and applies it to the current image. // jm at ibmp dot fr // checks if the current image can accept a lookup table. if (bitDepth==24) exit ("RGB images cannot have lookup tables"); // selects a file and checks if it complies with the announced Zeiss Confocal Palette file format path=File…

Normalized Variance

2008-10-24T11:46:08+02:00

A macro to determine image focal quality image-wide (not ROI-wide). // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-11 "Normalized Variance" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.3 // Date: 11/07/2006 // Author: Andy Weller macro "Normalized_Variance" { run("Clear Results"); run("Set Measurements...", " mean redirect=None decimal=5"); run("Measure"); mean = getResult("Mean"); selectWindow("Re…

PlateMontage

2010-01-26T11:01:44+02:00

Creates a labeled plate montage image from BD Pathway 855 / AttoVision 1.6 data sets /* PlateMontage macro */ var version = '1.4a, 2009-10-13'; // // Creates a labeled plate montage image from BD Pathway 855 / AttoVision 1.6 data sets // // Features: // Borders do not hide part of the images as in AttoVision // Simultaneous processing of up to three channels // Automatically saves the montage // Style is customizable // Well images can be inverted // Missing images are not a prob…

Radial Distribution Function

2009-05-15T21:08:35+02:00

An ImageJ macro that calculates the radial distribution function (RDF) of particle centers. Needs the Radial_Profile plugin. [Input image (left) and Radial Distribution Function (right)] The macro is based on the calculation of the autocorrelation via the Fourier transform, but it does not assume periodic boundary conditions. It increases the image size to a value large enough to avoid any influence of the 'periodic' nature of the FFT and corrects for finite-size effects (edge effects) that wo…

Radially Averaged Autocorrelation

2010-01-26T11:01:44+02:00

An ImageJ macro that calculates the radial average of the autocorrelation of a (binary) image. For the autocorrelation (radial distribution) of particle centers, see the Radial Distribution Function macro. [Autocorrelation plot for the input at left]

RGBtoHEX

2010-01-26T11:01:43+02:00

This simple macro exemplifies how to use ImageJ macro functions to convert RGB color values into Hex notation. ---------- Code: // This simple macro exemplifies how to use ImageJ macro functions to convert RGB color // values into Hex notation. // // After obtaining the RGB tripplet of the current foregound color, the macro prompts // the user to choose an alpha blending value. Choice is then converted into a four-byte // hex number (#AARRGGBB) that is copied to the clipboard and can be past…

ROI Color Coder

2009-12-15T05:13:54+02:00

This macro colorizes selections listed in the ROI Manager by matching measurements to a color of a lookup table (LUT). It generates particle-size heat maps. ---------- Output: [blobs.gif in which the Area of segmented particles was matched to the fire LUT (filled ROIs) and Feret lengths to a custom heat-map LUT (contours)]

Squared Gradient

2010-01-26T11:01:44+02:00

A macro to determine image focal quality image-wide (not ROI-wide) // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-2 "Squared Gradient" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.1 // Date: 14/07/2006 // Author: Andy Weller macro "Squared_Gradient" { W = getWidth(); H = getHeight(); sqGrad = 0; // Set to 0 which is out of focus for (j=0; j

Macros

2010-01-26T11:01:44+02:00

Standard Deviation-Based Correlation

2010-01-26T11:01:44+02:00

A macro to determine image focal quality image-wide (not ROI-wide) // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-13 "Standard Deviation-Based Correlation" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.1 // Date: 14/07/2006 // Author: Andy Weller macro "Corr_Stddev" { run("Clear Results"); run("Set Measurements...", " mean redirect=None decimal=5"); run("Measure"); mean = getResult("Mean"); selectWin…

Variance

2010-01-26T11:01:44+02:00

A macro to determine image focal quality image-wide (not ROI-wide). // A macro to determine image focal quality image-wide (not ROI-wide) // Based on algorithm F-10 "Variance" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // // Version: 0.1 // Date: 14/07/2006 // Author: Andy Weller macro "Variance_" { run("Clear Results"); run("Set Measurements...", " mean redirect=None decimal=5"); run("Measure"); mean = getResult("Mean"); selectWindow("Results"); run("Close"); …

ImageJ Documentation Wiki macro

Affine + Consistent Elastic 2D Image Registration

Auto Correlation

Brenner Gradient

Distribution Plotter

GFP-LC3

Import Zeiss lookup tables

Normalized Variance

PlateMontage

Radial Distribution Function

Radially Averaged Autocorrelation

RGBtoHEX

ROI Color Coder

Squared Gradient

Macros

Standard Deviation-Based Correlation

Variance