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Nuclear_Morphology / ui / Top bar

The top menu

The following menu options are available:


Option Action
New analysis > Use custom detection options Create a new morphology analysis
New analysis > Use custom detection options Run an analysis on images using saved detection options
Save workspace Save a group of datasets as a workspace for reopening together later
Open > dataset Open a saved .nmd dataset
Open > workspace Open a workspace
Save datasets Save all the open datasets
Save workspaces Save assignments of datasets into workspaces


Option Action
Options Choose display and logging options


Option Action
Pixels / Microns Choose the units for charts and tables. This requires a scale to be set for cells.
Colour swatch set the colour palette to use for colouring datasets and drawing segments in profiles. These swatches are:
1. Regular - a set of eight colours
2. No colour - all segments are black
3. Accessible - a set of colours chosen to be distinguishable in three major types of color blindness, Deutranopia, Protanopia and Tritanopia
Fill consensus fill consensus nuclei with a semi-transparent version of the dataset colour, rather than just showing an outline
Show task monitor Toggle the memory and task queue displays. The first shows the queue of tasks waiting to be performed (e.g. drawing charts). The second shows the amount of memory being used by the program. Free memory is green. Memory reserved by the Java Virtual Machine is orange, and memory actually in use is red. The percentage of memory actually in use is written.


Option Action
About Version and license information
Check for updates Check if an updated version is available for download
Open log directory Open the folder containing the program log files

Program options


The following options are available:

Option Description
Logging level set the logging of information to the log panel to be more or less detailed
Antialiasing this smooths the display of charts to remove jagged edges (note this does not change the data the charts are showing). It takes more resources, so can slow the program when analysing large datasets. It is on by default.
Convert datasets attempt to update older datasets to the latest format when opening