Microscope Control Feature: Multi-Dimensional Acquisition tool
By Mike Fussell, Life Sciences Product Manager
Published on Sep. 26, 2025
The free Zaber Launcher software is loaded with tools to make using Zaber microscopes and motion control products easy and intuitive. The Multi-D Acquisition tool, which is part of the Microscope app in Zaber Launcher, simplifies complex scans by combining XY tiling, Z stacking, illuminator and filter cube switching, and time lapse imaging.
What It Is
Multi-D Acquisition tool is a GUI based tool available in Zaber Launcher to quickly set up and run automated image acquisition sequences combining XY tiling, Z stacking, illuminator and filter cube switching, and time lapse imaging.
Figure 1. The Multi-D Acquisition tab in the Zaber Launcher Microscope app.
Like the other tools within the Zaber Launcher suite of free apps, the Multi-D Acquisition tool provides a simple and intuitive GUI to help you get the most from your Zaber devices, right out of the box. This tool supports the full range of Zaber Nucleus microscope systems from a single XY stage, to a complete system with focus stage, illuminator, objective changer, and filter cube turret.
The Multi-D Acquisition tool is not intended as a replacement for research-grade image acquisition like Starlyte Nebula, Inscoper or Visiview. There are three main limitations.
Only Zaber devices supported
Only devices supported by Zaber Launcher can be controlled by the Zaber Launcher microscope app. The Multi-D Acquisition tool can trigger cameras via digital IO, but it does not include integrated camera image display or settings control. To see the camera live view and change camera settings, you will need the software that came with your camera. IO triggering is very low-latency and helps maximize imaging throughput compared to the software triggering provided by other software tools.
Image processing not included
Zaber Launcher does not include any image processing capabilities. There are many excellent commercial and free image processing and analysis software packages available, and the images captured by your camera via triggering through Zaber Launcher can be processed by those tools.
Metadata export…Coming soon!
Zaber Launcher does not currently export metadata from the image acquisition sequence, but this feature is on the roadmap and will be added soon. This will provide a log of the complete acquisition sequence to support the traceability and reproducibility of your image data.
Why We Built It
A very common use case
Most Nucleus microscope users want to automate complex image acquisition sequences across multiple dimensions. These sequences, which require the coordinated operation of all Zaber hardware in a microscope system, include:
- capturing an array of image tiles to stitch into a single larger image
- imaging one or more positions at a repeating interval
- imaging one or more positions across a series of illumination wavelengths and filters
The high cost of commercial software
While there are multiple commercial software packages supporting Zaber Nucleus microscopes, they have a cost which may be outside the scope of a research budget, especially if they include powerful features that aren’t needed and wouldn’t be used for a project.
The steep learning curve of free alternatives
Free and open-source software, such as µManager, also supports Nucleus microscopes, but they can be time-consuming and complex for new users to set up and configure.
The performance penalty of existing tools
μManager incurs significant throughput penalties, slowing down the speed of data acquisition and limiting a lab's productivity. Zaber Launcher’s native support for Zaber devices and support for IO camera triggering minimizes latency to maximize throughput.
Who Is It For?
Our Multi-dimensional acquisition tool was developed with the following users in mind:
Users setting up their Nucleus microscope for the first time
With Zaber Launcher, you can start using your microscope straight out of the box. Zaber Launcher is a great way to validate your hardware performance before moving on to API control. Zaber Launcher detects Nucleus modules automatically and configures your microscope hardware, while an uncluttered and intuitive GUI eliminates the steep learning curve of open source software like μManager.
Users who only occasionally need multi-dimensional acquisition
If you only need to multi-dimensional image occasionally, or only need to automate one or two dimensions, the limited value delivered by commercial software may not justify its cost.
Users maximizing their throughput
Native Zaber device support and optimized motion profiles enables Zaber Launcher to deliver much higher throughput than software solutions like μManager. The tradeoffs made by μManager to support an impressively wide range of stages, cameras, shutters, filter wheels, light sources and more, result in high latency and reduced throughput.
Users engaged in fast prototyping or iterating quickly
Zaber Launcher is a valuable tool to quickly prototype and test solutions for R&D projects and for System Integrators. Users writing their own scripts or software for more complex automation can save time by setting up, testing and fine tuning their scanning plan in Zaber Launcher before they start programming.
How It Works
To acquire images via hardware triggering, connect a digital output from one of your Zaber devices to a digital input on your camera. Hardware triggering provides extremely low-latency communication directly between the Zaber hardware and the camera, which helps maximize throughput by minimizing communication delays as well as the polling needed to determine when a movement has finished.
Scans are set up by configuring each dimension sequentially. Dimensions that are not needed can be turned off.
XY grids and tiling
The XY Grid mode acquires images at user defined spacing which may have gaps in between. This is useful for applications like capturing one image per slide, or in the center of each well of a 96 or 384 well plate. XY Tile mode streamlines the capture of image tiles to be stitched. It automatically builds the scan pattern based on user selected start and end points and desired image overlap.
Figure 2. The Multi-D Acquisition tab in the Zaber Launcher Microscope app.
Focus control
The focus dimension is used to automate autofocus control and Z-stacking.The user can select different numbers of focal planes to be captured above and below their reference plane which can be useful when imaging adherent cells. If your system has an autofocus, that can be used before starting the Z-stack series. The autofocus can still be enabled even if no extra steps above or below the reference focus position are selected.
Figure 3. Z-Stacks can be configured with a different number of images above and below the starting focal plane.
Illumination and filters
Illumination and filter control is achieved by calling user-defined presets. Zaber Launcher’s microscope presets are a powerful feature which can be used to store collections of parameters. You can store as many settings as you want in a preset. Bundling filter and illuminator settings into fluorophore-specific channels is a common use.
Figure 4. Presets are a powerful tool that can bundle as many, or as few settings as you want into a single saved state. This enables you to create and switch between groups of highly specific or very general settings.
Presets can also include any combination of positions, motion parameters and objective selections.
Figure 5. Presets can be ordered however you like.
Order of operations
Once your desired dimensions have been selected and configured, they can be reordered.
Figure 6. Dimensions can be ordered however you like. The cycle time is displayed making it easy to see how changes in order will impact the cycle time.
Timelapse
Using the timelapse panel, you can set your acquisition sequence to repeat at regular intervals. The timelapse tool is useful for long duration live cell imaging.This feature is especially powerful when combined with the HL04 laser autofocus module to ensure samples stay in focus over a long acquisition sequence. To guarantee there is enough time for your acquisition sequence to execute completely before starting the next cycle, the tool will not allow intervals shorter than the cycle time.
Figure 7. The timelapse panel shows an estimation of both the individual cycle time and the complete sequence.
Summary panel
The summary panel provides useful information about the total number of images and total acquisition sequence time enabling you to make informed decisions about how to order your scanning operations. It will also help determine what your requirements for image storage and processing will be.
Figure 8. The summary provides a detailed breakdown of the number or images, scan area, cycle time and total time for your multi-dimensional acquisition.
Free tools from Zaber
Zaber Launcher’s free Multi-D Acquisition tool can save you time and money by helping you get new systems up and running quickly, rapidly prototype ideas, and test and optimize your scans before you start coding. This is just one of many powerful and easy to use tools included in Zaber Launcher which empower you to get the most out of your Zaber Nucleus microscopes and motion control products. You can learn more about Zaber Launcher here.