Fusion Acquisition Software

Deeper Insight, Better Data

• Visualise the 3D Structure of Your Sample​
• Flexible acquisition setup: choose the optimal order of channels and Z (Channels → Z or Z →Channels)​
• Compatible with piezo devices for fast and highly accurate Z‑scanning*1​
• Deep Z ^new - Option to increase laser power with depth ​
• maintain stable excitation and achieve uniform intensity in the imaging volume ​
• achieve Sharper deep-tissue detail due to reduced scattering and absorption of light within the sample.​

*1 Piezo available in Dragonfly Fusion only

Image Legend – The Deep Z feature in Fusion reveals hidden structures at depth
A Z‑stack was acquired (A, B), and the Deep Z feature was applied (A1, B1). In panels A and B, the laser power was kept constant at 6%. In panels A1 and B1, the laser power started at 6%and increased exponentially up to 30%. Deep Z activation occurred at approximately 80 µm depth, after which the laser power ramped progressively to 30%.​

A total of 231 stacks were acquired, corresponding to a 137‑µm imaging range. Structures that become visible due to the increasing laser power are indicated by the white arrows in A), A1)(MIP) and by the blue arrows B), B1) (orthogonal view).

Immediate experimental feedback ​

• Evaluate experimental progress as it runs​

• Allow accurate experimental judgment and decision in real time, ensuring your experiment stays on track

Grasp the dynamics of biology

Translate cell behaviours into biological insights by imaging dynamic processes in living cells.​

• Flexible definition of time lapse - Define time interval or number of repeats,​
• Repeat full time‑lapse protocols – Add additional protocol‑level repeat cycles for extended long-term experiments.​
• Finite burst – Execute ultra-fast time-lapse experiments and SMLM acquisitions*

*Available in Dragonfly only

Figure Legend – Time-lapse setup and results
(A) Easy time‑lapse setup: select the time interval and number of repeats. Focus stabilization can be activated for higher positional accuracy. The quad‑band filter enable seven faster image acquisition. (B) Mammalian cell division sequence: (B1) Prophase, (B2)Metaphase, (B3) Anaphase, (B4) Telophase. Microtubules are shown in red, and DNA in cyan.

Stay sharp. Stay confident. Stay in focus. ​

Fusion control hardware-based autofocus maintains sample focus throughout the experiment. This feature is critical for live imaging assays, multi-well plate imaging, large fixed samples, multi-position imaging, and multi-tile imaging.​

• Reliable​
• Straightforward setup.​
• Compatible with air and immersion objectives.​
• Available for Dragonfly and BC43 systems.​

Reliable. Accurate. Always in focus​

Multi-position Imaging of Mammalian Cells with BC43.
At each time point, four positions were captured in parallel, each with three channels and 15 Z‑stacks. Shown side‑by‑side, the video highlights how the Focus Seek & Lock technology keeps every position perfectly in focus—even during rapid multi‑site navigation. Image credits: Ines Baião‑Santos, Álvaro Tavares (Universidade do Algarve); Claudia Florindo (Oxford Instruments).​

Expand your imaging capabilities​

Configure multiple independent acquisition experiments and automate acquisition control for external devices.​

• Coordinate internal and external devices through REST API and Python scripts​

• Allow automation of microfluidics devices and acquisition​
• Allow a combination of independent protocols sequentially ​
• Possible to coordinate image analysis with acquisition through Python and Imaris ​

Note – This is an advanced feature, and its use requires an understanding of Python coding

Spatial omics graphic representation
With the power of our REST API, users can orchestrate complex workflows by linking multiple protocols and external devices. Comprehensive gene-expression atlases can be generated by coordinating our spinning-disk confocal systems (Dragonfly or BC43) with automated microfluidic triggering.

Effortless Sample Overview

See your entire sample instantly. With one click, our smart spiral montage delivers a complete, high-quality overview—no missed areas, no duplicate tiles.​

• Fast spiral acquisition from the centre outward​
• Flexible NxM layouts for any sample size​
• Expandable montage – if the stage is moved after the initial acquisition, new tiles seamlessly extend the existing montage.​
• XY Stage localisation – the eye icon complements the spiral montage, delivering visual information of the stage position relative to the montage.

Image Legend – Overview of sample navigation & spiral montage
A) A 2×3 spiral montage was acquired using the 2× objective. The navigation icon (arrow), the 2× objective selection (arrowhead), and the montage definition (green rectangle) can be observed. B) When switching to the 10×objective (arrowhead), the field of view is automatically adjusted (arrow).

See Beyond the Field of View

Unlock the complete perspective of your sample with seamless, high‑coverage imaging.​

• Comprehensive Tile Capture- Automatically acquire all relevant tiles to reveal the entire sample area — no details missed.​
• Flexible Montage Creation – Define montages by sample perimeter, or specify an exact number of tiles.​

Irregular montage ^new - Imaging That Adapts to Your Sample​

• Boost productivity, faster experimental progress ​
• Reduce image size by acquiring only the relevant tiles.​
• Design sample contours effortlessly using simple, intuitive tools. ​
• Capture flexible, non-rectangular regions that match real sample geometry.

NEW – Unlockhigher productivity by combining irregular montage with multiple positions

Figure Legend – Irregular montage increases productivity
This example compares a standard montage (left) with an irregular montage on the BC43 system (right). While the standard montage requires 1,040 tiles (2,080 images, 2 channels), the irregular montage reduces this to 646 tiles (1,292 images) by imaging only relevant sample areas.

The result is approximately 2× higher productivity for 2D imaging, with even greater gains for z-stacks and multi-channel acquisitions. For the same 3D sample, image count was reduced from 510,120 to 288,288, significantly decreasing acquisition time, data storage, and processing requirements.

In conclusion: Irregular montage acquisition captures only relevant sample regions, maximizing imaging efficiency while maintaining resolution and sample coverage.

Increase Productivity Through Higher Sample Throughput

Boost the efficiency of every experiment and extract more insight from each run.

1. More Output per Experiment - Deliver greater insight from every run without increasing workload.

2. Focus on What Matters - Acquire only the most relevant cells or sample regions to maximise efficiency.

3. Scale Further with Montage - Combine targeted acquisition with montage imaging for even higher coverage and context.

NEW – Unlock higher productivity by combining irregular montage with multiple positions.

Multiple positions increase experimental throughput​
In this time‑lapse, multichannel experiment, four positions were acquired to track mitotic cells, which can be rare depending on the tissue and cell line. The protocol included four confocal channels, time‑lapse, Z‑stack, and multi‑position acquisition with active focus stabilisation. Montage acquisition can also be added to further boost throughput.P1–P4 (right panels) show the four mitotic cells. Colour coding: dark blue – actin, pink – mitochondria, yellow – microtubules, cyan – DNA.

Redefine Throughput in Multi-Well Assays​

Efficiently image and analyse multiple experimental conditions, reducing turnaround time and increasing throughput.​

• Fast & high-quality screening - image at speed and without standing image quality. ​
• Take advantage of effortless Multi-well workflow and exceptional confocal performance. ​
• Flexible and compatible with different sample types, use what better suits your experimental setup: 6 to 384 well plates or chambered coverslips.​
• Scalable data capture pair with montage imaging to increase experimental results.

NEW – Unlockhigher productivity by combining irregular montage with multiple positions

One click well selection​

Navigate with well plate view or table view
All protocol combinations are possible.

Keep every field in focus

Enables correction of tilt and sample unevenness. Can be used in multi-position protocols.​

• Compatible with both single montage and multi-position protocols.​
• Ensures consistent focus across large imaging areas.​
• Increases throughput by acquiring only in-focus planes.​
• Reduces photobleaching by minimizing the number of planes required to capture all relevant data.​

Supports robust acquisition of uneven and complex samples.

Figure Legend – Focus Map Correction of Slide Tilt and Sample Unevenness
Twelve tiles of the Ascaris sample were acquired. (A) Due to tilt in the slide, the left side of the image is not well focused and appears less visible. (B) After applying the Fusion Focus Map to the tilted Ascaris sample, both the left and right regions of the specimen appear sharply in focus.

Illuminate Function, Frame by Frame​

An integrated, precise, and flexible photostimulation workflow for advanced functional imaging.​

• Direct control of the Mosaic DMD photostimulation device for precise light delivery.​
• Flexible pattern design to match experimental needs and sample geometry.​
• High spatial and temporal precision for accurate stimulation of targeted regions.​
• Enables a broad range of experiments including FRAP, photoactivation, and uncaging.​
• Real‑time through‑series analysis gives instant experimental feedback​

Compatibility: Dragonfly + Mosaic systems.

Perform Precise Photostimulation
Take precise control of photostimulation delivery. Target areas of tissues, individual cells or intracellular features. Gain insights into processes within living cells with powerful techniques such as photoactivation, FRAP, uncaging and optogenetics.

Simple, and accurate B-TIRF control.

B‑TIRF (Borealis TIRF) brings precision TIRF imaging to every user by simplifying a traditionally complex technique. With effortless setup and smart control, it delivers consistent, high-contrast and uniform illumination for demanding single-molecule and membrane-level studies.​

• Simple - and accessible to all users.​
• Versatile - enables the adjustment of the TIRF angle for different wavelengths within a single experiment.​
• Flexible - Compatible with both 60x and 100x objectives.​
• Reliable - a feedback loop sensor determine the precise TIRF position.

B-TIRF

Widefield

SMLM or SRFF-Stream​

Single‑molecule localization microscopy (SMLM) or push‑button super‑resolution—whichever fits your workflow.​

SMLM – Single‑Molecule Localization Microscopy​

• Enabled through Fusion’s Finite Burst Imaging mode​
• Achieves resolutions down to 10 nm​
• 3D‑SMLM provides true molecular‑scale information in all three dimensions​

(SMLM available for dragonfly only)​

SRRF‑Stream – One‑Click Super‑Resolution​

• Instant super‑resolution at the press of a button​
• No special sample preparation required​

Achieves resolutions down to 140 nm

Microtubules in a cell imaged using Single Molecule Localization Microscopy
A 10,000 time‑point series was acquired to capture the stochastic emission of Cy3 fluorophores. The data were rendered, drift‑corrected, and subsequently localized, achieving a median localization precision of ~13 nm. Image acquired with the Andor Dragonfly spinning disk confocal. Data courtesy of Felix Rivera‑Molina, Yale University.

Sharper images, more detail, improved resolution.​

ClearView^TM deconvolution enhances image clarity by removing haze and improving resolution.

• Sharper details – reveal hidden features in your image​
• Achieve greater scientific accuracy in image analysis results, including volume measurements and co-localisation.​
• Fast – GPU based – 50x faster than conventional CPU based algorithms​
• Easy – protocol activated- get your results swiftly after the image acquisition is finished.

Widefield + Deconvolution

Widefield

Enhanced resolution and contrast with ClearView™ deconvolution.​
Widefield images of a mammalian cell acquired on the BC43 system demonstrate the improvement in contrast and spatial resolution achieved through ClearView™ deconvolution. Left: Widefield image , right: deconvolved image. Deconvolution was activated in the protocol. Fluorescent labels: actin (dark blue), microtubules (yellow), mitochondria (pink), and DNA (cyan). Image credit: Claudia Florindo, Oxford Instruments.