Imagej Macro

One of them involves temporary files which are written into the temporary directory that ImageJ defines. A Novel ImageJ Macro for Automated Cell Death Quantitation in the Retina. the m button starts the measurement on the active. (Since you asked the same question on the ImageJ mailing list, there is a chance that this will change in the future. More plugins Links; ImageJ site; Another ImageJ site This one emphasizes ImageJ2. cm not in pixels?. • Developed ImageJ Macros to optimize image analysis on mammograms • Created various Matlab scripts to optimize lab processes • Awarded Summer Undergraduate Research Program Fellowship for. A: It occurs when the Java version used for ImageJ (Java 1. Java based imaging software and widely discussed in open source forum. The interesting part is that, in calculating each pixel, you can work with the previous intensity of the pixel (and even its individual red, green and blue components in case of a color image). It is not necessary to learn OpenCL itself. With ImageJ 1. The latest version of the plugin has problems running with the macro, an older version is here. ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health in the USA. Apply your macro to a group of images. Featuring screenshots of the free download of ImageJ. Macros are often used to achieve a goal in Outlook more quickly. Valente a Lucas A. Functions are provided for finding the minimum and maximum value of an array, appending and adding a value at an arbirary location, information about occurences of a value and printing of an. The easiest way to create a macro is to record a sequence of commands using the command recorder (Plugins ▷ Macros ▷ Record…↓). ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images and supports most major formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". xxx for ImageJ-32bit in MacOS X, Java 1. ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ. These macros can also be used for tiff images generated by other techniques (e. on image of a known scale and ask imageJ to make automatic lengh measurements for me from point 1 to 2, 2 to 3 and so on. LegacyCommandline handleBatchExit, handleBatchOption, ij1Helper, isBatchMode; Methods inherited from class org. x Examples Process Folder (IJ1 Macro) Example script to count nuclei in multiple images in a folder/subfolders: /* * Macro to count nuclei in multiple images in a folder/subfolders. number", "0");. A workshop for getting started with Fiji. I am trying to record a macro on Fiji (ImageJ). Selected downloaded IJM file 5. The original macro supplied with the publication (see below) doesn't work as-is. macro(マクロ)とは、ImageJで一連のコマンドを自動化するシンプルなプログラムのことである。マクロを作成するもっとも簡単な方法は、command recorder(コマンドレコーダー)を使って、一連のコマンドを記録することである。. For example, a macro can be written that ac-quires an image every 10 seconds and. Mitochondria are shaped by opposing fission (division) and fusion events. What can be especially useful is to record a macro and then set it up in such a way that you can batch process a bunch of images in one directory, and output with the. More plugins Links; ImageJ site; Another ImageJ site This one emphasizes ImageJ2. ImageJ の使い方については「ImageJで始める画像解析」という本が良書です。画像データの基本などの初心者向けの内容から入り、生物系の顕微鏡画像の具体的な定量解析や、有用なプラグインの活用法まで書いています。. • Documentation for yourself and other future users is helpful. But when I try a similar thing with VLC, the following works fine in a WinXP shell (opening the "USB 2861 Device" PAL camera in VLC), but doesn't work if I put it inside status=exec() as an imageJ macro. Open your image stack. A: It occurs when the Java version used for ImageJ (Java 1. The easiest way to create a macro is to record a series of commands using the command recorder. For this I have to make a list and pass the name of each image to the macro. The macro gets a line profile plot and fits to a the simple Gaussian function coded in ImageJ. 用imagej分析全球陸地日夜溫差,以NASA Earth Observations為例 這篇文章算是延續幾年前的這篇《 用imagej分析海溫,以NASA Earth Observations為例 》,但是會多一些工具的教學,像是利用影像運算,將日溫和夜溫計算出日夜溫差變化。. A workshop for getting started with Fiji. txt in the ImageJ macros folder (the same place you found it). Beamforming macros ImageJ macros to automate OptiNav beamforming software. To install the tools, drag the link Velocity_Measurement_Tool. getOptions() returns a String of macro options specific for the Thread in which the call is made. zip ‏1556 KB. Both approaches are available as KNIME plugin (currently beta status) and will be described in detail below. The coefficients of variation between macro and average of observers were approximately half the value of those between observers, for both ONL and INL dataset. BoneJ plugins are designed to be called from ImageJ macros, to make them easy to run on a whole directory of images. Beamforming macros ImageJ macros to automate OptiNav beamforming software. tif data sets, convert them to 8 bit and save the results in a directory chosen by the user. The macros are applied in the order they have been added. The section on that option on the ImageJ documentation wiki explains that if you want to change the pixel values rather than setting the minimum and maximum for the stack, you need to select the "Normalize" option. These tools are now available via the quantixed ImageJ update site. Select "Angiogenesis Analyzer" by clicking on the "toolsets" menu icon (>>) of the ImageJ tool bar. These images do not need to be open in ImageJ already—they will be read in as part of the batch process. ImageJ has an easy-to-use macro-language that means that knowledge of Java isn’t required for writing simple scripts. It gives a structure in five parts to your code, provides code for all input/output, and code for some usefull functions. CMCI ImageJ Macro Course 2. ImageJ is an excellent public domain imaging analysis platform that can be very easily used for almost all your image processing needs. 2 A Brief History of ImageJ and Fiji pg. In this part, you will create a macro to count the cells and calculate areas, circularities, mean intensities, as well as centroids in multiple images. Valente a Lucas A. In this case its the original image. txt file that came with ImageJ, that can be dropped in the ImageJ/macros folder that is created when you install ImageJ. Macro will. CMCI ImageJ Macro Course 2. Often you want to apply a common operation to all images in a given directory. For each frame of a time series, grey values along a line type Region Of Interest (ROI) that you specify by hand drawing are read out. Valente a Lucas A. This chapter is far from an extensive introduction to macro-writing, but rather aims to introduce the main ideas quickly using a worked example. The easiest way to create a macro is to record a series of commands using the command recorder. • To assign a macro to a start key: macro “name [key]" insert lines of code } Note that the function keys (F1-F12) are popular keys to assign to a start function. Comments and instructions can (should?) be written right into the macro file. Together these files take up under 5 MB. The macros can be downloaded from the. A macro is saved as a text file and executed by selecting a menu command, by pressing a key or by clicking on an icon in the ImageJ toolbar. ActionEvent e) Handle menu events. Scripts and macros are numbered with arabic numerals included in parentheses (e. More plugins Links; ImageJ site; Another ImageJ site This one emphasizes ImageJ2. • To assign a macro to a start key: macro "name [key]" insert lines of code } Note that the function keys (F1-F12) are popular keys to assign to a start function. Several mechanisms are at work to exchange data between these plugins. Th on a directory of cropped, binary image stacks. 7 The Command Finder. Robb b Fereshteh Moradi a Jeffrey A. and in the case of dual-color analysis. I am trying to record a macro on Fiji (ImageJ). ImageJ/Fiji becomes a image-processing librairie of Matlab. 1a) can be installed by recording the file available at this link in the "toolsets" repertory of the ImageJ distribution as. The ImageJ tool bar aspect should appear as showed below:. Copy carefully and be prepared to modify. Olympus to Fiji Stitch Converter. 1 Setting the Measurement Criteria Under the "Analyze" menu select "Set Measurements". PlugIn for ImageJ Introduction. One of them involves temporary files which are written into the temporary directory that ImageJ defines. But when I try a similar thing with VLC, the following works fine in a WinXP shell (opening the "USB 2861 Device" PAL camera in VLC), but doesn't work if I put it inside status=exec() as an imageJ macro. xxx for ImageJ-32bit in MacOS X, Java 1. ImageJ has a macro recorder that can record any actions that you make using the ImageJ menus into a new script: Ensure you are ready to start recording, for example have your image open Select Plugins > Macros > Record. Learn how to create a button for your macro to make the macro even more productive. 58 KB: 1384: 387cd4674f46000d3a3fa7b362a71834: MRI_Wound_Healing_Tool. These macros range from tools through macros that apply functions to every image pixel, to measurement of image parameters and drawing tools. One option, the “Find Maxima …” method, determines and counts the local intensity maxima in an image. Macro will. The names of the written files are StackRegSource; StackRegSourceR. LegacyCommandline handleBatchExit, handleBatchOption, ij1Helper, isBatchMode; Methods inherited from class org. The macro will open in an ImageJ macro editor window (named “Clipboard”) that has a Debug menu. Macros: You can create and debug macros that will automate the tasks used most often. - Batch processing using ImageJ macros (output is written to disk) - Number of detected particles is displayed - Absolute threshold can be set instead of relative percentile - The intensity momenta or order 0 to 4 are computed and output. Select the "MRI Wound Healing Tool" toolset from the >> button of the ImageJ launcher. Feel free to register and contribute additional content to the portal. ImageJ / Fiji Tutorials - Basics Revised for 2018 Table of Contents pg. BoneJ plugins are designed to be called from ImageJ macros, to make them easy to run on a whole directory of images. Open your image stack. - Duration: 31:22. To modify the AMCap. TIF converter. ImageJ has a macro recorder that can record any actions that you make using the ImageJ menus into a new script: Ensure you are ready to start recording, for example have your image open Select Plugins > Macros > Record. Placing the macro in the plugins folder, will cause the macro to appear in the plugins menu. On Linux and Windows, use the control key instead for keyboard shortcuts. Macros are basically sequences of commands, written in some programming language (here ImageJ's own macro language), which can be run automatically to make processing faster and easier. This HOWTO will guide you through the steps of setting up ImageJ to be aware of Jython, the Java implementation of Python 2. The interface of the plugin is a modal dialog that resembles the one implemented in ImageJ for batch macro execution. ActionEvent e) Handle menu events. A Novel ImageJ Macro for Automated Cell Death Quantitation in the Retina. How to write a macro in ImageJ/Fiji to repeat the same operation on several images? I want to create a macro that will repeat the same process (overlay) several images from two different sets of. I would be very grateful if you could help me create a macro in image J: - I open images in format (z000x_t000y, where y stays constant) that I want to. What I need to know is how can I write a macro that tells FIJI (or ImageJ) to overlay Fluorescent1 with DIC1, Fluorescent2 with DIC2, so forth so forth. Populates the module's input values, when the command is invoked from an ImageJ 1. - Duration: 31:22. Adding scale bars to images using ImageJ. To install the tools, drag the link Measure_Wound_Healing_Coherency. jPOR is easy to use and requires no knowledge of specific thin sections or specialist computer training. ImageJ is an excellent public domain imaging analysis platform that can be very easily used for almost all your image processing needs. ImageJ Fiji starts to cut out leaf discs from the top left corner of the first row, continues to the right and then starts with the next row. ImageJ plugins/macros. Create a new folder "Emory ICI" in your plugins folder of your ImageJ/Fiji software. Both approaches are available as KNIME plugin (currently beta status) and will be described in detail below. This HOWTO will guide you through the steps of setting up ImageJ to be aware of Jython, the Java implementation of Python 2. To use/write a custom macro just use the 'Pure Code'-filter. After downloading the latest version of the plugin, extract the contents of zip into the /ImageJ/Macros/ folder. Previous Workshop Materials. txt" and paste your new macro at the bottom of the file. Motivation. s/ImageJ/macros/ folder. Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube. C:\Program Files\ImageJ\macros and can also be installed as a menu item as well as assigned a keyboard shortcut. Save Macro file to Plugins / Utilities folder 6. IntroductionGUIMacro LanguagePlugin ProgrammingConclusionsResources ImageJ / Fiji Short Introduction into Macro and Plugin Programming ZOI Friday seminar. The same analysis can be obtained using a fluorescent staining by calcein. ) Use the getProfile() macro function to get the list of values (as shown in this example macro), or use Plot. The macros can be downloaded from the. ImageJ runs either as an online applet or as a downloadable application which you'll find here. Does anyone know what code I could use to have the macro threshold each image at the top 2% of each. This work presents FISHji, a set of new ImageJ methods for automated quantification of fluorescence in images obtained by epifluorescence microscopy. Tips for using ImageJ by G. txt, restart FIJI, and your macro should appear under the file menu Plugins > Macros. CLIJ reference for ImageJ macro. Email neil. The glasbey. We used ImageJ as the platform of choice for development of an image processing algorithm in the form of ImageJ macros. Send comments to wsr nih. CLIJ is an OpenCL - ImageJ bridge and a Fiji plugin allowing users with entry-level skills in programming to build GPU-accelerated workflows to speed up their image processing. Development 2. However, the. The location of this directory can be examined by issuing the macro command 'print(getDirectory("temp"));'. Use the Command Recorder (Plugins>Macros>Record) to generate run() function calls. It is not necessary to learn OpenCL itself. Robert Bagnell and Dr. Someone in the lab asked me to write a macro that saves values of "Plot Profile" function in ImageJ for a stack of images. The macros are applied in the order they have been added. A Novel ImageJ Macro for Automated Cell Death Quantitation in the Retina. The Intensity Macro for Background Subtraction is customized for the image processing and analysis done by the Ogle Lab. Hello everybody. Overcoming limitations. net is full of ImageJ development and analysis resources. This is the best way to install these macros and maintain the latest versions. In order to use the greyscale-watershed method (the w-button) you must have the Watershed Algorithm installed. BoneJ A plugin for bone image analysis in ImageJ which uses Local Thickness. With the release of ImageJ version 2 ( ImageJ2 ) comes the ability to run scripts in " headless " mode, which means that ImageJ can be launched without a GUI from the command prompt and variables parsed to the script. Tips for using ImageJ by G. Since there is no categorized index, you might want to use the search facility on this page. Disclaimer. We used ImageJ as the platform of choice for development of an image processing algorithm in the form of ImageJ macros. See the ImageJ website at NIH for more information and the latest upgrades if you are using it something beyond the lab 12 exercise. Moved Permanently. ImageJ/Fiji becomes a image-processing librairie of Matlab. Keep in mind we have modified the ij. Placing the macro in the plugins folder, will cause the macro to appear in the plugins menu. jpg image that you downloaded in the Intro to ImageJ section. A macro is a simple program that automates a series of ImageJ commands. 3 Updating ImageJ and Fiji and increasing available memory pg. calling a macro within another macro I've created a macro that applies a set of processes to an image and now want to apply this macro to a set of images within a loop. Alexander Fedorov 10,543,402 views. txt Convert large tif files to 8 bit. ) Use the getProfile() macro function to get the list of values (as shown in this example macro), or use Plot. I agree with Quora User. lut (direct link) can be used to colorize selections randomly (although other strategies would probably perform better in this task, e. ImageJ is an excellent public domain imaging analysis platform that can be very easily used for almost all your image processing needs. Image Processing with ImageJ is a practical book that will guide you from the most basic analysis techniques to the fine details of implementing new functionalities through the ImageJ plugin system, all of it through the use of examples and practical cases. x Examples Process Folder (IJ1 Macro) Example script to count nuclei in multiple images in a folder/subfolders: /* * Macro to count nuclei in multiple images in a folder/subfolders. Download Macro File 2. two-channel images of polarity-sensitive membrane dyes such as Laurdan and di-4-ANEPPDHQ. Macro basics & built-in functions. From the checkboxes have ONLY the “Grey Mean Value” checked. The Introduction into Macro Programming explains the principles of macro writing. imagej-macros. Images can be sourced from either a digital film scanner or. Since there is no categorized index, you might want to use the search facility on this page. ImageJ の使い方については「ImageJで始める画像解析」という本が良書です。画像データの基本などの初心者向けの内容から入り、生物系の顕微鏡画像の具体的な定量解析や、有用なプラグインの活用法まで書いています。. c++,templates,macros,typedef. s/ImageJ/macros/ folder. The macro keeps the registered position, in the example (2290, 1. xxx for ImageJ-32bit in MacOS X, Java 1. Macros: You can create and debug macros that will automate the tasks used most often. The names of the written files are StackRegSource; StackRegSourceR. For examples, see the ArgumentPassingDemo macro. jPOR is a macro toolset designed to work with the ImageJ public domain image processing program to allow the rapid measurement of porosity using prepared thin section images. Plugins and Macros created for ImageJ by Dr. The coefficients of variation between macro and average of observers were approximately half the value of those between observers, for both ONL and INL dataset. Working Subscribe Subscribed Unsubscribe 415. PURPOSE: TUNEL assay is widely used to evaluate cell death. De Novo Software has provided two ImageJ macros that will help you export your image analysis from ImageJ to FCS Express Image Cytometry. In addition, capability to access single pixels allows you to analyze details of. ImageJ MacroBlocks Generator. Calculator Plus Plugin in ImageJ with Batch>Macro Hi Everyone! I'm trying to use a Macro to subtract a set of images from a specific image (Background Image) with Calculator Plus plugin. Access to ImageJ for AS/DS 434. Summer Session Combines ImageJ Basics and Intermediate ImageJ into one class, so you only need to attend one session! ImageJ Macros. The names of the written files are StackRegSource; StackRegSourceR. 2 A Brief History of ImageJ and Fiji pg. Image processing with ImageJ : discover the incredible possibilities of ImageJ, from basic image procesing to macro and plugin development. Does anyone know what code I could use to have the macro threshold each image at the top 2% of each. Suppose you wish to gather measurements from an image using real values (µm, miles, etc). LegacyCommandline handleBatchExit, handleBatchOption, ij1Helper, isBatchMode; Methods inherited from class org. This macro can be saved using the Create button to save the macro with the name specified in the “Name” field. Use the segmented line tool to create a line selection that outlines the DNA contour. How to write the macro for draw rectangle so that the coordinates and dimensions are in units e. It gives a structure in five parts to your code, provides code for all input/output, and code for some usefull functions. Select "Angiogenesis Analyzer" by clicking on the "toolsets" menu icon (>>) of the ImageJ tool bar. jar file and the files in the macros and plugins folders to make commands specific to the 434 laboratory. The ImageJ macro language itself does not support storing custom preferences. I cannot find how to introduce the use of the mouse for a ROI rectangular selection. TIF converter. Summary: I wrote a macro for the ImageJ program to automatically measure particle shapes on a photograph. ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ. for common 3D tasks - Extensive suite of scripts/plug-ins developed by scientific community • Macro language enables rapid construction of automation workflows. Featuring screenshots of the free download of ImageJ. A macro is a simple program that automates a series of ImageJ commands. Does anyone know what code I could use to have the macro threshold each image at the top 2% of each. From these sections 21 images were taken randomly of each heart. ijm to the ImageJ launcher window, save it under macros/toolsets in the FIJI installation and restart FIJI. stack macro language. A workshop for getting started with Fiji. Because of this, there is a considerable amount of ImageJ inspiration that has gone into QuPath's design, and a conscious decision made to try to make QuPath more immediately accessible to. The particle sizes are then processed to plot a size distribution of the powder. Macros are basically sequences of commands, written in some programming language (here ImageJ's own macro language), which can be run automatically to make processing faster and easier. Figure 1 shows the analysis of MCP-GFP β-actin 3′UTR mRNA particle movements in a living cell over time (see Movie 1). ImageJ macro to calculate general polarization (GP) values from microscopy images, e. xxx for ImageJ-64bit in MacOS X and all the window-versions) is not compatible with the Java version used for compiling this plugin (Java 1. The full ~100MB download comes with several large sample data sets, which are helpful for getting started but not required for the software to run. Human-in-the-loop Particle Analysis, beta: batch particle analysis followed by user selection of desired particles. Th on a directory of cropped, binary image stacks. To avoid this use the 64-bit ImageJ in Mac. It is a complete rewrite of ImageJ, but includes ImageJ1 with a compatibility layer, so that old-style plugins and macros can run the same as always. It looks for new and updated "Macros" (including "Examples"), "Tools" and "Toolsets", and installs them. txt to the plugin folder or the macro folder and restart ImageJ. December 6, 2013 August 4, 2011 by Krishna Mohan. Macros are basically sequences of commands, written in some programming language (here ImageJ's own macro language), which can be run automatically to make processing faster and easier. This macro is for measuring the width of a bright linear structure such as the connection between two cells, a blood vessel, or an aerial view of a road. Select 'Crop' from the Add Macro Code drop-down menu 5. For the 16th time we will organize the ImageJ workshops at the University of Leicester. Optical Density Calibration. HyperStackReg. Open the macro in the Fiji Script Editor, type cmd-A (Select All), cmd-C (Copy), close the Script Editor and type cmd-V (Paste). The Angiogenesis Analyzer is a simple tool to quantify the ETFA experiment images by extracting characteristic information of the network. Methods inherited from class net. Disclaimer. Alexander Fedorov 10,543,402 views. The single leaf discs are labeled with the title of the scan and a number (Titelscanimage_1, Titelscanimage_2, etc. ImageJ is scriptable software!. To install the tools, drag the link Velocity_Measurement_Tool. jPOR is a macro toolset designed to work with the ImageJ public domain image processing program to allow the rapid measurement of porosity using prepared thin section images. Place each of the plugins you need into this folder and they'll appear under Emory ICI in the plugins menu. Using it in a point and click fashion works great however it can be even more powerful when you learn how to automate tasks such as the analysis of multiple images ImageJ to increase the efficiency and reproducibility of your science research. It runs on any computer with a Java 1. File Date Size D/L MD5; ImageJ Macros 15/05; MRI_Fibrosis_Tool. I wanted to read numbers in a text file and use them in my ImageJ macro. This is a system to help you in ImageJ macro writing. Macro will. No new dates available, please email [email protected] macro threshold values. , resetMinAndMax(). I cannot find how to introduce the use of the mouse for a ROI rectangular selection. • Documentation for yourself and other future users is helpful. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. 4) the axial FWHM (resolution along the z-axis: 𝐹𝑊𝐻𝑀. 1: Loading a stack of images to Fiji: Image files can be drag and dropped to Fiji's interface, then each image is opened in its own window. jPOR is easy to use and requires no knowledge of specific thin sections or specialist computer training. They can be launched via the Macros --> Run Macro menu that appears at the top of the macro text window (in ImageJ). PURPOSE: TUNEL assay is widely used to evaluate cell death. These files are provided for use under the Open Software License v. Together these files take up under 5 MB. ImageJ has a macro recorder that can record any actions that you make using the ImageJ menus into a new script: Ensure you are ready to start recording, for example have your image open Select Plugins > Macros > Record. This is the ImageJ toolbar. A imageJ macro to refine my hematoxylin/eosin stains for islets of Langerhans in pancreas sections imagej macros microscope Star Updated Jun 1, 2018. Lastly, although ImageJ Macro processes with a speed comparable to Javascript and Jython, it is slow compared to Clojure and Scala. ImageJ image processing or measurement tasks can be packaged within macro text files to speed and automate analysis tasks. Instructions for how to follow a 3rd party update site are here. Macro functions and code snippets are typed in monospaced font, e. The coefficients of variation between macro and average of observers were approximately half the value of those between observers, for both ONL and INL dataset. ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ. Because it was necessary to modify the original ImageJ code to enable some of these features, this package should be installed in its entirety. edu with questions and/or requests for updates/changes. ImageJ performs the necessary steps to create a maximum intensity projection and kymograph. Installation: Download Comet_Assay. Summer Session Combines ImageJ Basics and Intermediate ImageJ into one class, so you only need to attend one session! ImageJ Macros. jPOR is a macro toolset designed to work with the ImageJ public domain image processing program to allow the rapid measurement of porosity using prepared thin section images. In this part, you will create a macro to count the cells and calculate areas, circularities, mean intensities, as well as centroids in multiple images. txt, restart FIJI, and your macro should appear under the file menu Plugins > Macros. macros and plug-ins. 5 Installing a plugin manually (ImageJ and Fiji) pg. FIJI: Writing an ImageJ macro. MBF_ImageJ was developed by Tony Collins and colleagues to provide a comprehensive user manual with an organized preloaded plug-in and macro structure for ImageJ so that users could follow the. Maddalena a Ellen L. To install the tools, drag the link Adipocyte_Tools. lut (direct link) can be used to colorize selections randomly (although other strategies would probably perform better in this task, e. Spatial calibration of an image using FIJI. txt” in the folder where the original image is saved. ijm to the ImageJ launcher window, save it under macros/toolsets in the FIJI installation and restart FIJI. It is old and simple in appearance but don't underestimate its ability. File Date Size D/L MD5; ImageJ Macros 15/05; MRI_Fibrosis_Tool. Some simple macros for Fiji/ImageJ that we are using in the lab. Mitochondria are shaped by opposing fission (division) and fusion events. From these sections 21 images were taken randomly of each heart. The sequence of commands is written into the macro file. Open Fiji (ImageJ) 3. Help with an imagej macro? I don't have any experience with Imagej, so any help at all would be greatly appreciated. The first step in calibrating the image is to measure the mean gray value of the background and the first 18 steps.