https://imagejdocu.list.lu/ 2026-11-09T18:13:10+00:00 https://imagejdocu.list.lu/ https://imagejdocu.list.lu/lib/tpl/dokuwiki/images/favicon.ico text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/affine_consistent_elastic_registration?rev=1555067621&do=diff Affine + Consistent Elastic 2D Image Registration 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 text/html 2022-11-18T15:03:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/analyze_stripes?rev=1668780198&do=diff Analyze_Stripes Analyze_Stripes is a Fiji (or ImageJ) macro designed to automatically measure the width, edge roughness, and orientation angle of stripes. Introduction The Analyze_Stripes macro was developed for scanning electron microscopy (SEM) metrology of electron beam lithography written stripes. However, the macro is useful to anyone who needs to analyze stripe widths, edge roughness, and orientation angle. The result is an average of nearly all of the edge pixels within the region of… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/autofocus_hyperstack?rev=1555067621&do=diff // Autofocus hyperstack macro // Select the in focus frame from each slice of a hyperstack and create a new stack // of just the in focus frames // Based on algorithm F-11 "Normalized Variance" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // And the original macro by Andy Weller http://imagejdocu.tudor.lu/doku.php?id=macro:normalized_variance setBatchMode(true); //Get image type type = bitDepth(); if (type==8) {type="8-bit";} else {if(type==16) {type="16-bit";} else… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/auto_correlation?rev=1555067621&do=diff Auto Correlation 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<H; j++) { for (i=0; i<W;… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/basic_diffusion_analysis?rev=1555067621&do=diff //Example macro that does a diffusion analysis on a results table of tracking data //The required format is as generated by the Manual Tracking plugin //http://rsbweb.nih.gov/ij/plugins/track/track.html //assuming Results Table column headings; Track > Slice > X > Y //It requires many tracks and many time points! //Plots the cumulative mean squared displacement (MSD) per time point //For a more accurate approach see the time ensemble average example dis2 = 0; for (i=0; i<nResults(); i++){ if … text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/brenner_gradient?rev=1555067621&do=diff Brenner Gradient 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<H; j++) { for (i=0; i<W; i++) { p… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/calculating_stats_from_a_results_table?rev=1555067621&do=diff //Example macro calculating stats from a results table column //Import any data into a results table and then use the following to extract summary stats //The examples use "Area" as the column heading //All results checked with OpenOffice Calc, note: variance uses n-1 to correct for sample bias //Some variables N=0; total_area=0; mean_area=0; total_variance=0; variance_area=0; SD_Area=0; SE_Area=0; CI95_Area=0; max_area=0; min_area=0; //Generate a results table run("Clear Results"); run("Blobs… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/diffusion_analysis_time_ensemble_average?rev=1555067621&do=diff //Example macro that does a diffusion analysis on a results table of tracking //data. The required format is as generated by the Manual Tracking plugin //http://rsbweb.nih.gov/ij/plugins/track/track.html //assuming Results table column headings: Track > Slice > X > Y //It requires many tracks and many time points! //The analysis uses the time ensemble average method described in Charsooghi, MA et al 2011 //http://www.sciencedirect.com/science/article/pii/S0010465510003620 //Get number of trac… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/distribution_plotter?rev=1555067621&do=diff Distribution Plotter Plots relative and cumulative frequencies on a double Y-axis graph of a measured parameter. Description * Part of BAR * Retrives relative and cumulative frequencies * Fits a Normal distribution to the histogram of relative frequencies text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/gfp-lc3_macro?rev=1555067621&do=diff GFP-LC3 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. text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/importzeisslut?rev=1555067621&do=diff Import Zeiss lookup tables 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 P… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/import_metamorph_screen_acquisition_tile_data?rev=1555067621&do=diff Stitch data from MetaMorph 7 "Screen Acquisition" module Reassembles tiling data acquired by MetaMorph into stacks and hyperstacks. MetaMorph 7's Screen Acquisition (screenacq) does not natively support time and Z acquisitions from it's UI or journal functions. Therefore it's easier to assemble the 5D experiment (x,y,z,t,c) with FIJI including stitch TIF files together with overlap. text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/lsmtorgb?rev=1555067621&do=diff Convert selected channels from LSM files to RGB LSM files should open as composite images or hyperstacks. That is usually the most convenient formats, but in some rare cases it might be necessary to convert them to RGB images. (example: the Puncta_Analyzer plugin requires RGB input images.) text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/mitpophagy_mitochondrial_morphology_content_lc3_colocalization_macro?rev=1555067621&do=diff Mitophagy Mitophagy 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. Also, GFP-LC3 puncta that colocalize with mitochondria is a way to measure the initiation of mitochondrial autophagy, the catabolic process by which mitochondria are targeted for lysosomal degradation. text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/multiple_points?rev=1555067621&do=diff Export / Import Multi-point set Bellow you can find two macros aimed to work with multi-point set in ImageJ/Fiji. Basically user just uses the default tool “multi-point” to select some points in image and then using this macro he can simply export them into TXT file (used format is compatible with text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/normalized_variance?rev=1555067621&do=diff Normalized Variance 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("Mea… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/open_multiple_images_at_once?rev=1555067621&do=diff Open Multiple Images Introduction This short macro opens the indicated number of images within a folder in a sequential manner. This is useful if one desires to open multiple images at once for stacking or analyzing data with another macro Author text/html 2021-09-14T11:58:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/particle_in_cell-3d?rev=1631613505&do=diff Particle in Cell-3D Particle in Cell-3D is an ImageJ Macro designed to quantify the uptake of macro- and nanoparticles by cells. <Particle_in_Cell-3D processing overview. a) Representative confocal section image and orthogonal projections of a HUVEC cell membrane stained with CellMask™ Deep Red. b) The respective image of silica nanoparticles labeled with perylene, a fluorescent dye. The 3D location of an intracellular particle is marked by the crossing yellow lines. c) A smoothing filter is … text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/particle_properties_to_image?rev=1555067621&do=diff Particle Properties to Image An ImageJ macro that creates a new (floating-point) image where the pixel value of each particle (or one point at the center of the particle) is equal to a property of the particle. Dialog Parameters [screen shot] [For clarity, a Lookup Table and a Calibration Bar have been applied to the 'blobs.gif-Area' output using the Standard ImageJ commands] text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/platemontage?rev=1555067621&do=diff PlateMontage 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… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/plot_zeroed_tracking_data?rev=1555067621&do=diff //Plot tracking data from a results table zeroed //The required format is as generated by the Manual Tracking plugin //http://rsbweb.nih.gov/ij/plugins/track/track.html //assuming Results table column headings: Track > Slice > X > Y //some variables Track = 0; result = 1; //Plot the graph Plot.create("Scatter Plot", "X", "Y"); //You may want to determine your own limits in some way here Plot.setLimits(-250, 250, -250, 250); //Get number of tracks for (a=0; a<nResults(); a++) { if (getRes… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/radially_averaged_autocorrelation?rev=1555067621&do=diff Radially Averaged Autocorrelation 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] Description The macro calculates the text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/radial_distribution_function?rev=1555067621&do=diff Radial Distribution Function The Basics 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 … text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/rgbtohex?rev=1555067621&do=diff RGBtoHEX 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 c… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/roi_color_coder?rev=1555067621&do=diff ROI Color Coder Colorizes selections listed in the ROI Manager by matching measurements to a color of a lookup table (LUT), generating particle-size heat maps. It complements the Analyze>Analyze Particles... command. ROI Color Coder is part of the BAR. text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/squared_gradient?rev=1555067621&do=diff Squared Gradient 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<H; j++) { for (i=0; i<W; i++) { p … text/html 2021-05-04T13:42:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/start?rev=1620128520&do=diff Macros Pages in this namespace: * Affine + Consistent Elastic 2D Image Registration * Analyze_Stripes * Auto Correlation * autofocus_hyperstack * basic_diffusion_analysis * Brenner Gradient * calculating_stats_from_a_results_table * Convert selected channels from LSM files to RGB * diffusion_analysis_time_ensemble_average * Distribution Plotter * Export / Import Multi-point set * GFP-LC3 * Import Zeiss lookup tables * Macros * Mitophagy * Normalized Variance * Open Multiple … text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/stddev_correlation?rev=1555067621&do=diff Standard Deviation-Based Correlation 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"… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/tiled_autofocus_hyperstack?rev=1555067621&do=diff // Tiled autofocus hyperstack macro // Breaks down the image into ROIs of user defined size // Selects the in focus slice for each ROI (in each frame of the hyperstack) and creates a new stack // of montaged in-focus ROIs for each frame // Based on algorithm F-11 "Normalized Variance" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // And the original macro by Andy Weller http://imagejdocu.tudor.lu/doku.php?id=macro:normalized_variance //Get image details type = bitDep… text/html 2019-04-12T13:13:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://imagejdocu.list.lu/macro/variance?rev=1555067621&do=diff Variance A macro to determine image focal quality image-wide (not ROI-wide). Note (2011): please note that this macro is not really necessary as ImageJ already supports computation of the standard deviation via the same command used to obtain the mean image value: