Main menu bar
The following menu options are available:
| Option |
Action |
| New analysis > Use custom detection options |
Select a folder of images and start a new morphology analysis |
| New analysis > Use saved detection options |
Select detection options from a file, and a folder of images to start a new morphology analysis |
| New workspace |
Create a workspace to enable opening datasets in one batch. |
| Open > Open dataset |
Select a saved dataset in .nmd format to open. Note that you can also drag and drop an .nmd file into the software to open it. |
| Open > Open workspace |
Select a saved workspace in .wrk format to open. Note that you can also drag and drop a .wrk file into the software to open it. |
| Save selected |
Save the datasets currently selected in the populations panel |
| Save all |
Save all open datasets |
| Option |
Action |
| Scale |
Choose the display units for charts and tables. Pixels is the default unless overridden in the configuration file. Displaying measurements in Microns requires the image scale to be set for the dataset. |
| Colour palette |
Set the colour palette to use for colouring datasets and drawing segments in profiles. These palettes are: Regular - a set of bright exciting colours; No colour - all colours are black; 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 |
| Task monitor |
Toggle the task queue and memory displays. The first shows the queue of tasks waiting to be performed (e.g. drawing charts, running analyses). 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 displays the memory actually in use (the red section). Hover the mouse over the monitor to see the total available memory (or look at the log file). |
| Option |
Action |
| Add... |
Submenu with options for adding new data to a dataset; see below |
| Curate |
Launch the curation screen, so you can scan through cells one by one, and mark them as keep or reject. Desired cells can be saved as a child dataset. |
| Set scale |
Set the image scale for the dataset in pixels per micron |
| Merge |
Combine the cells from the selected datasets into one new dataset, and run a new morphology analysis. |
| Boolean |
Perform boolean operations between this dataset and another dataset. |
| Add to workspace... |
Allows datasets to be added to an existing workspace |
| Remove from workspace... |
Allows datasets to be removed from a workspace |
| Delete (child) |
Delete a child dataset from its parent. Only available if the selected dataset is a child dataset. This change is not saved to file automatically. |
| Close (root) |
Close a root dataset. Only available if the selected dataset is a root dataset. You will be prompted to save any changes. |
| Export... |
Submenu with options for exporting data; see below |
| Option |
Action |
| Add nuclear signal |
Detect nuclear signals in a set of images, and add them to the nuclei in the dataset |
| Post-FISH mapping |
Assign pre-FISH nuclei to categories based on FISH image data |
| Shell analysis ofsignals |
Begin a shell analysis of signals in the selected dataset |
| Warped signals |
Begin signal warping for a root dataset with nuclear signals |
| Child collection from file |
Create a child dataset based on the nuclei saved in a .cell file (these can be created via the Export submenu) |
| Cluster group from file |
Create a child dataset based on clusters defined in a text file in tab separated format |
This sub-menu contains commands for getting data out of the software for running your own downstream analyses.
| Option |
Action |
| Nuclear measurements |
The measured values for each nucleus, plus normalised profiles |
| Full nuclear profiles |
The non-normalised angle profile values for each nucleus. Since there are a different number of values in each nucleus, they are combined into a single column, separated by commas for later parsing |
| Full nuclear outlines |
The X and Y coordinates of each border point in the outline of each nucleus. Since there are a different number of values in each nucleus, they are combined into a single column. XY pairs are separated by commas for later parsing. Within each pair, X and Y values are separated by a pipe (|) e.g. 12.4|3.6,12.9|4.0. |
| Nuclear signal measurements |
The measured values for each nuclear signal |
| Nuclear signal shells |
The measured nuclear signal in each shell, following shell analysis |
| Consensus nuclei as SVG |
The consensus nuclear outlines of the selected datasets in SVG format |
| Cell locations within images |
The XY coordinates of nucleus centres-of-mass within their source image |
| Dataset analysis options |
The options used to analyse this dataset in XML format. This can be used directly to set up subsequent analyses |
| Single cell images |
Export each nucleus as a separate image to a folder in the same directory as the nmd file. You will be given the option to mask out background; if this is selected, any pixels not within the nucleus will be set to black. |
| Cell locations within images |
The image name and centre of mass of each nucleus |
| Dataset analysis options |
The options used to detect nuclei in the selected dataset. Can be used as an input to replicate the same analysis on another folder of images. |
| Landmark rulesets |
The rules used to detect landmarks, so you can make your own detection rules |
| Option |
Action |
| Open user guide documentation |
open this file |
| Check for updates |
Check if an updated version is available for download |
| Open config file |
Open the configuration file in the default text editor. Allows you to set some default options (e.g. image scale, scale display, default folders) |
| Open config directory |
Open the folder containing the program log files, configuration options and landmark detection rulesets |
| About |
Version and license information |
