README.md

Spotmetrics

Spotmetrics is an open-source Image-Analysis software plugin for automatic chromatophore detection and measurement. This software has been published on the Frontiers In Physiology Journal and more information about its purpose and use can be found there.

Already Have Fiji Installed ?

Having Fiji already installed is great and will lower the amount of time it will take to get Spotmetrics setup.

Proceed to Install Spotmetrics

Install Java, Fiji and Spotmetrics

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.

• Download & Install Java Here
• Make sure Java was installed correctly
  • Visit Oracle's Verify Java Version Page
  • If your browser blocks the Java web-plugin then visit the Oracle's Manual Java Check Page

Proceed to Install Fiji

Install Fiji

Java is installed and now we can proceed with installing Fiji.

Go to Fiji's download page and download the latest version of Fiji. Make sure to download the "No JRE" version. This will ensure that Fiji will always use the latest verison of Java that is installed on your system.

Install Spotmetrics Plugin

1. Exit Fiji if it is already running
2. Download the latest version of Spotmetrics Jar file Here
3. Download all dependency Jar files
   • tablelayout.jar
   • poi-3.14-20160307.jar
   • poi-ooxml-3.14-20160307.jar
   • poi-ooxml-schemas-3.14-20160307.jar
   • xmlbeans-2.6.0.jar
4. Place the Spot_Metrics.jar file in Fiji's plugins folder Fiji.app\plugins
5. If prompted to replace an existing file, click on "Yes"
6. Place all the dependency jar files in Fiji's plugins folder Fiji.app\plugins
7. If prompted to replace existing files, you do not need to replace them
8. Start-up Fiji

Verify Integrity of the downloaded files (optional)

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

• md5: 244926976BD4245F0F41946941FECAE0
• sha1: 75F740C5C44B26DFEF473537517E46876027FADC
• sha256: E019ED9B64BD1408B4650CE924F82766A3876F841DC2B2382F19F5BB9E925196

An online check tool can be used like Online MD5

Screenshots

Configuration Tabs

Spot Tracks

Results & Overlays

Authors

• George El-Haddad
  • Software Engineer
• Stavros Hadjisolomou
  • Principal Investigator

License

Copyright © 2017 George El-Haddad & Stavros Hadjisolomou

Licensed under the General Public License version 3.0

• http://www.gnu.org/licenses/gpl-3.0.en.html
• https://tldrlegal.com/license/gnu-general-public-license-v3-(gpl-3)