Tools for connecting objects
In many cases, you may want to connect objects together, for instance, the same cell through a time lapse video, or spots to a nucleus. These connections can be made manually using connection tools such as Lasso connect or also automated connection algorithms such as Connect to Nearest. Connections can also be deleted manually. These connections can also sometimes be made when a property is computed to show you what objects were used in the computation.
Best practices for connections
Use tags effectively: Properly tagging your objects makes connection tools more precise
Assign hotkeys: Set up hotkeys for your most frequently used connection tools
Think about directionality: Remember that connections have direction (parent to child) which can be important for certain analyses
Connections form the foundation for many powerful analyses in NimbusImage, enabling you to quantify relationships between objects and trace structures across time.
Manual connection tools: click and lasso connect
NimbusImage provides several intuitive tools for manually creating and removing connections between objects:
Click connect
The Click connect tool allows you to create connections between objects by simply clicking them in sequence:
First, click on a "parent" object
Next, click on a "child" object
A connection will be established from the parent to the child
This tool is ideal for precisely connecting specific objects, like linking individual RNA spots to their corresponding cells or connecting organelles to their parent structures.
Configuration options:
Parent Annotation Tags: Filter which types of objects can be selected as parents
Child Annotation Tags: Filter which types of objects can be selected as children
Filter by layer: Optionally restrict selections to objects on specific layers
Lasso connect
The Lasso connect tool allows you to quickly connect multiple objects at once:
Draw a lasso around all the objects you want to connect
NimbusImage will automatically establish connections between the selected objects
This is particularly useful for:
Connecting multiple spots to a cell at once
Connecting sequential points in a time-lapse track
Creating connections between groups of related objects
In time-lapse mode, the Lasso connect tool will intelligently connect objects sequentially by time point, making it extremely valuable for track creation and repair.
Click disconnect
The Click disconnect tool allows you to remove individual connections:
Click on a connected parent object
Click on its connected child object
The connection between them will be removed
This is useful for removing incorrect connections without affecting other valid connections.
Lasso disconnect
The Lasso disconnect tool allows you to quickly remove multiple connections at once:
Draw a lasso around the connected objects
All connections between objects within the lasso will be removed
This is particularly helpful when you need to clear all connections in a region and rebuild them correctly.
Automated connection tools
NimbusImage provides powerful automated tools that can establish connections between objects based on various criteria, saving you considerable time compared to manual connections.
Connect to nearest
The Connect to nearest tool automatically connects objects based on spatial proximity:
Each object with the "parent" tag will be connected to its nearest object(s) with the "child" tag
The connections are established based on configurable distance and relationship criteria
Configuration options:
Parent tag: Tag that identifies which objects will serve as parents in the connections
Child tag: Tag that identifies which objects will serve as children in the connections
Connect across Z: When enabled, allows connections between objects on different Z-slices
Connect across T: When enabled, allows connections between objects at different time points
Connect to closest centroid or edge: Choose whether to measure distance from:
Centroid: The central point of each object (faster, simpler)
Edge: The boundary of each object (more precise for irregularly shaped objects)
Restrict connection: Apply additional constraints to connections:
None: Connect based solely on distance
Touching parent: Only connect children that physically touch their parent
Within parent: Only connect children that are completely contained within their parent
Max distance (pixels): The maximum allowed distance between parent and child objects
Connect up to N children: Limit the number of children that can connect to each parent
This tool is particularly useful for:
Connecting RNA spots to their nearest nucleus
Assigning cells to their closest blood vessel
Connecting subcellular structures to their parent cells
Efficiently processing large datasets with many objects
Connect timelapse
The Connect timelapse tool specializes in automatically tracking objects across sequential time points:
Objects with the same tag are connected from one time frame to the next
Connections are established based on spatial proximity between frames
The algorithm intelligently handles object movement between frames
This is especially valuable for cell tracking, particle movement analysis, and other time-dependent studies.
Configuration options:
Object to connect tag: Specifies which objects to track across time points (all objects with this tag will be connected)
Connect across gaps: Allows connecting objects even when there are missing time points
Set a value from 0-10 to determine how many time points can be skipped
For example, a value of 1 would connect an object at t=5 directly to t=7 if t=6 is missing
Max distance: The maximum pixel distance objects can move between frames and still be considered the same object
Set this based on how much your objects typically move between frames
Lower values (5-20 pixels) work well for slow-moving objects
Higher values may be needed for rapidly moving objects or lower frame rates
How it works:
The algorithm processes each spatial location (XY, Z) separately
For each time point, it searches for the closest matching objects in subsequent time points
Connections are created from later time points to earlier ones (children to parents)
All connections are automatically tagged with "Time lapse connection" for easy identification
This tool is perfect for:
Automatically generating cell lineage trees
Tracking particle movement over time
Analyzing cell migration patterns
Measuring growth or movement rates
Best practices:
Start with a small max distance (10-20 pixels) and increase if needed
Use the "Connect across gaps" feature when you have intermittently missing objects. These can be later fixed manually using Time lapse mode
When tracking dividing cells, use this tool first, then manually correct division events
Review tracks in Time lapse mode to identify and fix any tracking errors
For very dense or challenging datasets, consider tracking a subset of objects first
After running the Connect timelapse tool, you can use the Time lapse mode (discussed in the Time lapse mode section) to visualize, review, and manually correct the resulting tracks.
Connect sequential
The Connect Sequential tool (in the Connections category) links each object to its nearest neighbor in the immediately preceding slice, either across time or across Z:
Objects with the chosen tag are compared slice by slice along the axis you pick (Time or Z)
Each object becomes a "child" connected to the nearest matching object in the previous slice (time point − 1 or Z − 1), which becomes its "parent"
Each object connects to at most one parent
Configuration options:
Object to connect tag: Specifies which objects to connect (all objects with this tag will be connected)
Connect sequentially across: Choose Time to connect objects from one time point to the next, or Z to connect objects from one Z-slice to the next (default: Time)
Max distance (pixels): The maximum distance between a child and its parent; objects farther apart than this are not connected (range: 0–5000, default: 1000)
How it works:
Objects are never connected across different XY positions. When connecting across Time, only objects in the same Z-slice are connected; when connecting across Z, only objects at the same time point are connected.
Distance is always measured between object centroids (for points, the point itself).
Created connections are tagged with the same tag as the input objects.
When to use it instead of Connect timelapse:
Use Connect sequential when you need to link objects across Z-slices (for example, following a structure through a Z-stack), since Connect timelapse only works across time.
Use Connect timelapse for most time-lapse tracking, especially when objects can be missing from some frames: Connect sequential only looks at the immediately preceding slice and cannot bridge gaps.
Browsing and editing connections
Once you have connections, the Connections tab in the Object Browser lets you see exactly what is connected to what, and clean up whatever is wrong — without hunting through the image for it.
trackId property.Two views of your connections
The Flat view lists individual parent-to-child links; the By track view groups them into tracks, where a track is a chain of connections following one object through time. By track is the natural view for time-lapse data; the flat list is more useful for spot-to-cell style connections.
A Scope selector controls which connections the tab shows:
All connections in the dataset
Current location — only connections at the XY position, Z slice, and time point you're viewing
Selected objects — only connections involving objects you've selected
Passing filters — only connections whose objects survive your current filters
Deleting connections
From the Connections tab you can delete a single link, an entire track at once (Delete track), or every connection currently selected (Delete selected). This makes it practical to fix a tracking run that went wrong in one region without discarding the whole thing. Each track row also has a Select action that selects that track's objects in the viewer.
You can also click connection lines directly in the viewer — in both normal and time-lapse mode — so if you can see a bad link, you can cut it exactly where you see the problem rather than searching for it in a list.
Connecting selected objects
The Connect selected action chains the objects you currently have selected into connections, in ascending time order. This is a quick way to build or repair a track from objects you've already picked out.
Labeling tracks with a computed track ID
By default, the by-track view titles each track with a short internal identifier. If you have run the Parent-Child Connection IDs property worker, that worker assigns each track a numeric trackId — and that is the number that shows up in your exported CSV. To make the panel agree with your exports, use the Track ID property select in the by-track view and pick the computed property path (for example, nucleus Connection IDs / trackId). Each track is then titled with that value — Track 42 — with the short internal id moved into the tooltip.
Because the worker assigned those ids against the connection graph as it existed when the property was computed, tracks whose connections have changed since then get a badge:
partial — the track has members the property never covered, so objects were added after the worker ran
mixed IDs — the track's members carry different ids, meaning two previously separate tracks have since been joined
no ID — none of the track's members have a value
These badges are useful in their own right: they point at exactly the tracks whose connectivity changed after your last property computation, which are usually the ones worth reviewing. Re-running the property clears them.
Filtering by track metrics
The Track filters menu — the filter icon beside the Flat / By track toggle — applies minimum and maximum bounds to three track metrics:
Connections in track — how many links the track contains
Objects in track — how many objects the track passes through
Duration (timepoints) — how long the track spans in time
This is the fastest way to find the tracks worth your attention: set a minimum duration to isolate long-lived cells, or a maximum to surface the short fragments that usually indicate a tracking failure.
A connection whose track falls outside an active bound disappears from the list and from the image — both the connection lines in normal mode and the tracks in time-lapse mode. While a filter is narrowing, the count reads "N of M", the filter button carries a badge, and the empty state tells you the track filters are responsible rather than implying the dataset is empty.
Track filters are view state for the current session, and they reset when you switch datasets — numeric bounds from one dataset rarely mean the same thing in another.
Also hide these tracks' objects in the image is an off-by-default checkbox in the same menu. With it on, the filtered-out tracks' objects are hidden too, not just their connection lines — useful for decluttering a dense field down to the tracks you care about. This is purely a display setting: the hidden objects still appear in the Objects tab, in exports, and in analysis. Objects that aren't part of any track are never hidden by it.
Cleaning up dangling connections
Over the life of a dataset, connections can end up pointing at objects that have since been deleted. These "dangling" connections do nothing useful but still count toward your totals and track metrics.
When NimbusImage finds any, the Connections tab shows a row offering to delete them across the whole dataset. It reports the live count, asks for confirmation first, and the deletion can be undone. On a dataset with no dangling connections the row doesn't appear at all.
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