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Nuclear_Morphology / ui / Populations Panel

The populations panel holds the list of datasets currently loaded, and allows sub-analyses to be run on them. The width of the populations panel can be adjusted using the slider between the log panel and the populations panel.

populations_panel.png

It lists the name of the dataset, the number of cells it contains, and the colour the dataset is represented by in multi-dataset displays. The header of the table shows the total selected number of datasets and cells.

Info Image
Two types of dataset can be represented: root datasets and child datasets. A root dataset is the top-level dataset in the tree; it is not a child of any other dataset. Child datasets have a parent dataset; either a root dataset, or another child dataset. root_and_child.png
The name of the dataset can be changed by double clicking the 'name' cell. If a proposed name exists in the panel already, the software will prompt you to choose a different name. rename_collection.png
The colour of the dataset for multi-dataset displays (e.g. profiles, boxplots, consensus nucleus outlines) can be set by double clicking the colour cell. By default, a colour is selected based on the position of the dataset in the list of all selected datasets: the first is blue, the second yellow, the third green etc. The default colour pattern is the same as the segment pattern colours. The default colour is overridden if a colour has been explicitly set. The colour will be remembered if the dataset is saved before the program is closed. change_dataset_colour.png

Right click popup menu

Right clicking the dataset will bring up a menu with further options:

Populations_popup_menu.png

Population panel menu options

Option Action
Move up and Move down Change the position of a root dataset in the list. It has no effect on child datasets.
Workspace... Allows datasets to be added to or removed from existing workspaces
Merge Combine the cells from the selected datasets into one new dataset, and run a new morphology analysis.
Delete or Close Close applies to root datasets, and you will be prompted to save changes. Delete applies to child datasets, which will be immediately removed from their parent. Deleting a parent will also delete all its children.
Boolean Perform boolean algebra between this dataset and another dataset.
Curate Go through cells one by one, and mark them as keep or reject. Desired cells are saved as a child dataset.
Save nmd as... Save an nmd file of the dataset to a specific location
Change folder Specify a new folder of images matching the nuclei in this dataset. Use e.g. if the .nmd has been copied to a new computer
Export... Has a submenu with options for exporting data; see below E
Set scale Set the image scale for the dataset in pixels per micron
Add... Has a submenu for adding nuclear signals or Post-FISH mapping

The Export submenu

This sub-menu contains commands for getting data out of the programs for running your own downstream analysis.

Details are described here

The Add submenu

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
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: Cell_UUID Cluster_number

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