CIMMYT MaizeScanner
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CIMMYT MaizeScanner

Already Have FIJI Installed ?

Already having FIJI installed is great and will lower the time spent getting started.

Go directly to the Install CIMMYT Maize Scanner Plugin section

Install Java, FIJI and Plugin

This section is for those users who need to install everything in order to get started.

Install Java

The very first step that needs to be done is to make sure that the latest version of Java is installed. Follow the steps below to install the latest version of Java.

Go to Install Fiji section

Install Fiji

Now that the latest version of Java is installed we can proceed with installing FIJI.

  1. Download the latest version of FIJI Here
    • Make sure to download the "No JRE" version

Install CIMMYT Maize Scanner Plugin

  1. Download the CIMMYT Maize Scanner Jar file Here
  2. Download the dependency Jar file tablelayout.jar Here
  3. Place the CIMMYT_Maize_Scanner.jar file in Fiji's plugins folder\plugins
  4. Overwrite any existing version of the jar when or if prompted to
  5. Place the dependency tablelayout.jar jar file in Fiji's plugins folder\plugins
  6. Start up Fiji

Verify Integrity of the downloaded files (optional)

Provided are 3 hash codes to check the integrity of the file CIMMYT_Maize_Scanner.jar

  • md5: 0DABCA3BF75730DE41D0AD753C1BDD77
  • sha1: E03AC17B5316567125130958FBD8AE7EF49C36C4
  • sha256: FF4A82E64F1E699CC0E9BCD6AC63A3E0809BD14ED479FEC40D6C5F86BE635E1D

An online check tool can be used like Online MD5

Installing Auto-Run Script

The CIMMYT Maize Scanner Plugin can be auto-run when FIJI starts. To do this follow the instructions below to install the auto-run script.

  1. Download the auto-run script file Here
  2. Create a folder called AutoRun inside Fiji's "macros" folder \\macros
  3. Place the downloaded macro autorun_cimmyt.ijm in the AutoRun folder that was created in step 2
  4. Start Fiji and the plugin should auto-run



Image processing tab shows various processing options to enable on the batch selection of images


Image analysis tab allows the researcher to define an unlimited number of particle analysis passes as well as save a summary of the results in excel format and option to save the analysis overlays for each image analyzed.


Canopy macros tab runs a default batch macro on a defined set of images. More macros can be added that will allow the user to customize the macro and add their own vegetation index calculator


NGRDI & TGI macros to run on a defined set of images


Maize MLN scans macro


Maize MLN fields macro


BreedPix tab that will process batch images through the breedpix algorithm and optionally output GA/GGA imagees


Customize your CSV output with delimiter of your choice


  • George El-Haddad
    • Software Engineer
  • Dr. Shawn Kefauver
    • Project Principal Investigator



Copyright 2015 Shawn Carlisle Kefauver

Licensed under the General Public License version 3.0