Projects

Save and restore your entire Nexus session - panel layouts, workspace organisation, timeline position, notes, and more - as a .nexus project file.

Overview

A Nexus project file (.nexus) captures the complete state of your session so you can close the application and pick up exactly where you left off. Project files are lightweight SQLite databases that store references to your source data files rather than duplicating the data itself.

Source data files (.dm3, .emd, .csv, etc.) must remain accessible on disk for the project to reload correctly. The .nexus file does not embed raw data.

What gets saved

Category	Details
Panel layout	Which panels are open, their positions, sizes, and which signals are displayed
Workspace	Folder structure, signal groupings, custom colors and labels
Timeline	Current time position, crop range, playback speed, visible signal tracks
Source file references	Paths to all loaded data files (absolute + relative for portability)
Signal metadata	All imported signal information needed to reload data on demand
Notes	User-created notes with timestamps
Annotations	Signal annotations and overlays configured on panels
UI preferences	Dark mode, sidebar state, and other UI settings
Signal offsets	Manual time offsets applied to signals

Saving a project

Save (`Ctrl` + `S`)

If the project has been saved before, it overwrites the existing .nexus file.
If this is a new project, a Save As dialog appears so you can choose a location and filename.

Save As (`Ctrl` + `Shift` + `S`)

Always opens a file dialog, allowing you to save a copy of the current project under a new name or location.

Unsaved changes indicator

When you make changes after saving (adding signals, moving panels, editing notes, etc.), Nexus shows that the project has unsaved changes in two ways:

A green ● dot appears next to the project name in the header bar.
The window title updates to include the dot - for example, ● My Project - Nexus.

Once you save, the dot disappears and the window title returns to normal.

Closing with unsaved changes

If you try to close Nexus while the project has unsaved changes, a confirmation dialog appears with three options:

Button	Action
Save	Saves the project (or opens Save As if it hasn’t been saved before), then closes
Don’t Save	Discards unsaved changes and closes immediately
Cancel	Returns to the application without closing

Loading a project

Open Project (`Ctrl` + `O`)

A file dialog opens filtered to .nexus files.
Select a project file and click Open.
Nexus clears the current session and restores the saved state.

What happens during load

Current data is cleared - all loaded signals and panels are removed.
Source files are resolved - Nexus checks that the original data files still exist on disk, first via their absolute path, then by relative path from the project file location.
Metadata is restored - signal metadata is loaded back into the backend so signals can be visualised.
Signal data is loaded on demand - only signals referenced by visible panels and timeline tracks are fully parsed from disk.
UI state is restored - panels, workspace, timeline, notes, and all other settings are applied in a single update.

Missing source files

If any source data files have been moved or deleted since the project was saved, Nexus displays a Missing Source Files dialog listing the files it could not find. The project continues loading with the available files; panels referencing missing data will be empty.

Once this dialog appears, your previous session has already been cleared as part of the load process. You cannot return to it from this dialog.

Nexus stores both absolute and relative file paths. If you move the project file together with its data files (keeping the same folder structure), relative path resolution will find them automatically.

Merged DM3/DM4 datasets in projects

When a project contains merged DM3/DM4 datasets, Nexus handles them transparently:

Saving - each individual DM file in the merged series is tracked separately with its own path, while preserving the merged group association.
Loading - all member files are resolved individually; if every file is found, the merged dataset is reconstructed automatically. If any member file is missing, the entire merged group is reported as missing.

New Project

Select New Project from the nexus menu or use Ctrl + N to start a fresh session. This clears all loaded data, panels, workspace organisation, and timeline state.

If the current project has unsaved changes, the unsaved changes dialog appears first so you can save your work before starting fresh.

File format details

The .nexus project file is a standard SQLite database with the following structure:

Table	Purpose
`sections`	JSON blobs for each state category (timeline, workspace, canvas, notes, etc.)
`source_files`	Individual source file references with absolute paths, relative paths, and file sizes
`schema_version`	Format version for future compatibility

This format is designed for durability and forward compatibility - older project files will continue to load in newer versions of Nexus.