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Nuclear_Morphology / Installation

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Installation and configuration

This section contains information on installing, removing and customising the program.

Installing

Nuclear Morphology Analysis is designed to be runnable on Windows, Linux and MacOS, though it has been primarily designed and used on Windows. Since it requires a Java runtime, there are two ways to run the software

  • with an included packaged Java runtime
  • with a user installed version of Java (16 or higher)

Windows

Option Link Info
Portable Nuclear_Morphology_Analysis_2.1.0-windows.zip Software and Java runtime in a portable format. Unzip the folder wherever you like and run 'Nuclear_Morphology_Analysis.exe'.
Installer Nuclear_Morphology_Analysis_2.1.0-windows.msi Software and Java runtime in an installer for Windows. This will add the software to your list of installed programs, and create a start menu entry. May require administrator privileges depending on where you install.
Standalone Jar file Nuclear_Morphology_Analysis_2.1.0.jar The jar file with all dependencies for users who want to use their own Java install.

You can also download a set of images suitable for testing the software from https://bitbucket.org/bmskinner/nuclear_morphology/downloads/Testing_mouse_image_set.zip.

Linux

Option Link Info
Linux portable Nuclear_Morphology_Analysis_2.1.0-linux.tar.gz Software and Java runtime in a portable format. Extract the folder wherever you like and run 'launch.sh'. This version was packaged on Debian 11 with glibc 2.31. If you have issues with the packaged version, install Java 16 or higher and use the standalone jar below.
Standalone Jar file Nuclear_Morphology_Analysis_2.1.0.jar The jar file with all dependencies for users who want to use their own Java install.

You can also download a set of images suitable for testing the software from https://bitbucket.org/bmskinner/nuclear_morphology/downloads/Testing_mouse_image_set.zip.

MacOS

The software is not currently available packaged with the Java runtime. You will need to:

Due to security permissions in recent versions of MacOS (Catalina and above) the program won't have access to user folders if launched by double-clicking the jar file. You should launch from the Terminal; open the Terminal, navigate to the directory containing the jar file, and launch the jar using java -jar Nuclear_Morphology_Analysis_2.1.0.jar.

You can also download a set of images suitable for testing the software from https://bitbucket.org/bmskinner/nuclear_morphology/downloads/Testing_mouse_image_set.zip.

Uninstalling

Windows installer version

  • Go to Programs and Features, find Nuclear Morphology Analysis in the list of installed programs, and click 'Uninstall'
  • Nuclear Morphology Analysis also creates a folder in your home directory called .nma. Delete this folder too to remove all traces of the program.

Portable versions - Windows, Linux and MacOS

  • Delete the folder containing the program.
  • Nuclear Morphology Analysis also creates a folder in your home directory called .nma. Delete this folder too to remove all traces of the program.

Configuration and user data

Nuclear Morphology Analysis creates a folder in your home directory called .nma on first launch, if this folder does not already exist. The folder is used to store:

  • log files
  • built-in rulesets for shapes we can detect
  • custom rulesets for novel shapes you want to analyse
  • custom program options

You can open the configuration folder via Help > Open config directory.

Logs

The system state is logged when NMA is started in case debugging is needed. None of the logged data leaves your computer unless you explicitly send it. If you do find a bug or have a problem, and get in touch via the issue tracker you can upload a log file and it may help me track down the problem. There will be up to 5 log files, with nma.0.log containing the most recent logs.

Rulesets

Rulesets are how we identify landmarks in nuclei. The program has default rulesets for mouse sperm, pig sperm and round nuclei. These are stored in XML format. If you delete one of the default files, it will be recreated when the program is next launched.

Custom options

Custom options are set in the config.ini file in the configuration directory. They are in the format OPTION=VALUE. The following options can be set, and will take effect when the program is next launched:

Key Allowed Values Effect
DEFAULT_IMAGE_SCALE A positive number e.g. 18.0 Sets the default scale for converting pixels to microns
DEFAULT_COLOUR_SWATCH REGULAR_SWATCH ACCESSIBLE_SWATCH NO_SWATCH Sets the default colouring of datasets and segments
DEFAULT_DIR directory with backslashes escaped e.g. C:\\path\\to\\folder Sets the default folder for exporting data
DEFAULT_DISPLAY_SCALE PIXELS MICRONS Sets the default scale to display in charts and tables
REFOLD_OVERRIDE true false If true, the 'best-fit nucleus' method will always be used instead of the position averaging method
USE_ANTIALIASING true false Sets the default value for the 'Use anti-aliasing' option. False makes charts faster to render, but not as pretty.
USE_DEBUG_INTERFACE true false If true, shows debugging information in some charts
USE_GLCM_INTERFACE true false If true, allows GLCM measurements for nuclei
FILL_CONSENSUS true false Sets the default value for the 'Fill consensus' checkbox in the view menu
CHECK_FOR_UPDATES true false If true, the software will check for new versions on launch. If false, updates can still be checked manually via Help > Check for updates
USE_SINGLE_THREAD_DETECTION true false If true, the software will only read a single image at a time. If false, several images will be analysed in parallel

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