Structured illumination spinning disk microscopy


Clarity instrument Control Software

Visionary is Aurox's proprietary software designed specifically for the set-up, control and review of imaging experiments using the Aurox Clarity.

visionary software

Visionary Experiment types and modes:

Z-stack imaging

Whether you want a fast single Z-stack in up to 4 colours or a series of multi-channel Z-stacks as part of a tile-scan and or timelapse experiment, set-up couldn't be easier with full control over:

  • Z-stage range
  • Sectioning
  • 1 to 4 colour channels

Timelapse imaging

Simply define a Z-stack and enter the duration and repeat frequency for your timelapse.

Tilescan imaging

Drag out a wireframe over the required area to define the tilescan. Define the Z-stack settings and away you go.

Combine it with a timelapse experiment too.

Fast multi-channel imaging

Set-up, up to 4-colour channels for any given experiment. Define the exposure and intensity settings for each channel and everything else is automatic.

Need more than 4 channels? Use a multi-band filter cube installed in Clarity and use our custom version Aurox MicroManager software.

clarity door open showing filter cube

Multi-position ROI imaging

Simply drag out multiple wire frame boxes over multiple regions of interest (ROI). Then define the Z stack and any timelapse.

Real time live imaging

Aurox products use spinning disks, making imaging fast. Visionary shows you a real time live image of the sample on the microscope stage.

Worried about bleaching? Pause the live view at anytime, turning off the illumination.

Multi-colour inspect / review

Want to check you images? When your experiment ends, Visionary automatically switchs to inspect mode allowing you to step through and review the images either as colour cast individual or combined channels.

Adjustable sectioning

Choose between widefield or confocal. Choose between three levels of sectioning (Z-resolution levels). Switching sectioning modes is as easy as clicking a button.

Available modes are:

  1. High Signal/Low Sectioning
  2. Medium Signal/Medium Sectioning
  3. Low signal/High Sectioning
  4. Widefield

Z resolutions for the chosen sectioning mode and objective lens are handily displayed.

aurox confocal microscope visionary-adjustable-sectioning.jpg

Ease of use:

Easy set-up

Whether it's Clarity or associated devices including lights sources, cameras, stages and filters set-up is quick and easy within Visionary.

A graphical map of the hardware is displayed together with drop down menus for each device. Simply, select the device an its graphic outline colour changes from red to green.

Auto-calibration of Clarity completes within 5-10 secs.

aurox confocal microscope aurox visionary hardware set up tab.jpg

Colour coded guided workflow

All you have to do is start at the top follow the workflow down the control tab. Separate function areas, are colour coded for ease of follow:

  • Red for in software help and warnings
  • Yellow for Z stack settings

Need some help with the best settings including exposure times, light source intensity and camera binning? Check out Visionary's histogram.

aurox visionary software colour coded workflow

Detailed help tab

Need some guidance? Simply, pull up a detailed explanation and advice at any time using the in software help tab. Visionary is also supported by a detailed User Manual and Step-by-step training videos accessible on our YouTube Channel.

aurox confocal microscope Visionary-help.jpg

One click image export

Exporting image data is as easy as one click. Simply click on the filename or filepath at the top of the Visionary screen and the image is exported as an OMETIFF together with companion file.

The images and companion file can then be read directly into a third party image processing software.

If ImageJ is installed on the computer running Visionary then image data will automatically open in ImageJ following 'One Click Export'.

Automated calibration

The Aurox Clarity instrument has a built in calibration system. On starting the Visionary software or on changing to the calibration tab, Clarity will attempt to auto-calibrate using the current or stored settings.

User interaction is typically only required for the initial set-up and alignment of Clarity on the microscope and the initial set-up of the Visionary software, unless the set-up has been changed.

aurox confocal microscope aurox visionary calibration screen.jpg

3rd party device control

Visionary supports an increasing range of third party devices which can be attached to your microscope and used in combination with the Aurox Clarity to achieve laser-free confocal or widefield imaging.

Current and historical devices supported include:

  • Many makes and models of microscope stage
  • LED and metal halide light sources
  • CCD and sCMOS cameras
  • Sample stages
  • Piezo motor Z controllers

Visionary is built on a back bone of MicroManager software. If a MicroManager driver exists for a device, that device can be easily added to Visionary.

visionary software

Continuous support & development

The Aurox software team are continuously working on Visionary, adding new functionality, improvements and supported third party devices. What we do, is largely guided by user feedback and requests received through our email address, recorded and tracked in our software support database.

Feature requests are assigned to upcoming planned Visionary update releases.

Inevitably, new updates of Visionary will contain bugs not caught by our extensive in-house testing before release. Bug fix version releases are made from time to time as required.

New Visionary version updates are typically released every 6-months and are available free for download to our registered users through our software download web page.


Supported Cameras and Light Sources

The table shows all devices currently supported by Aurox Visionary software for use with Clarity / ClarityHS. If support for other devices is required, please contact us.

CamerasLight sources
Hamamatsu Orca Flash 4.0 V3 CoolLED pE300Ultra
Hamamatsu Orca Flash 4 LT CoolLED pE4000
Hamamatsu Orca Flash 4 V2 (USB 3.0) Excelitas X-cite 120 PC-Q
PCO Panda Excelitas X-cite 120 LED
PCO Edge 5.5 USB3 Andor AMH200
Photometrics 95 Prime BSI Lumencor Sola
Photometrics 95 Prime B Lumencor Spectra-X
Andor Zyla 5.5 USB Prior Lumen 200


Aurox Ltd
Culham Science Centre
Oxfordshire. OX14 3DB.
Tel: +44 (0)1865 407814