Light Microscopy

The Bioimaging Platform offers researchers access to a range of high performance confocal and widefield fluorescence microscopes. Capabilities include live imaging of cell dynamics and multichannel imaging of stained cells, 3D cultures, tissues and small organisms. Support in advanced fluorescence techniques such as FLIM, FRET, FRAP and FCS is also available for quantitative analysis of interactions and mobility of molecules in cells.


Confocal imaging

Zeiss LSM 980 Upright Spectral Laser Scanning Confocal (Arriving Q3/Q4 2023)

The Zeiss 980 has two sensitive detectors and four lasers (405, 488, 563, 633 nm) for sample excitation and imaging. It also features a 32-channel spectral detector, as well as a choice of eight high-resolution objectives (5 -100x), including three dipping lenses.

Use it for multichannel fluorescence in animals (e.g. Zebrafish, drosophila) or plants, Z stack 3-D reconstructions and extended focus images, and for creation of tiled mosaic "overview" images. Employ spectral imaging and unmixing to discriminate multiple overlapping fluorescence emission profiles at once.

Zeiss LSM 900 (formally 800) Airyscan Laser Scanning Confocal (Upgrade Q3/Q4 2023)

The Zeiss 800 Airyscan confocal is being upgraded to a modern Zeiss 900.

This inverted instrument is equipped with four lasers (405, 488, 563, 633 nm), six high-resolution objective lenses (10x, 20x, 25x multi immersion, 40x water, and 40x and 63x oil), sensitive detectors, a Definite Focus auto-focus module and an incubation system with CO2 and temperature control. The 900 is used for multi-channel fluorescence imaging of fixed tissues, as well as stable long-term live-cell imaging work. Enhanced resolution below the diffraction limit (to about 140 nm) is possible in SR mode by utilising the 32 channel Airyscan detector (1.7-fold resolution improvement = 120 nm).

A high resolution monochrome camera fitted to this microscope also facilitates rapid widefield imaging and navigation of large areas of interest.

Andor Dragonfly 202 Spinning Disk Confocal  (Arriving June 2023)

The Andor Dragonfly 202 delivers outstanding multi-dimensional images from the subcellular (nm) to whole organism (cm). Coupled with dual Andor Sona sCMOS cameras its unrivalled combination of speed and sensitivity allows researchers to image dynamic events at high temporal resolutions and image live organisms for days.

Integrated super-resolution (<100nm) solutions via SRRF-Stream+ with confocal and widefield are possible with the press of a button. Furthermore, it incorporates the newly developed High Power Laser Engine (HLE) with 7 laser lines and Borealis illumination to allow more even illumination from UV-Vis to NIR and thus more usable data across the field of view. An integrated OKO live cell chamber and Nikon TiE2 inverted microscope with eight available objective lenses and perfect focus system allows for long term, high-resolution imaging of cells and animals.

Zeiss LSM 780 Laser Scanning Confocal

The Zeiss 780 inverted microscope has seven laser lines for sample excitation and features three photo multiplier tubes, a 32-channel spectral detector, a choice of five high-resolution objectives (10-100x) and live cell incubator.

Use it for multichannel fluorescence imaging of cells (live or fixed), 3-D reconstructions and extended focus images for imaging of 3-D cultures via confocal Z stacks, and tiling for creation of mosaic "overview" images of larger samples. Employ spectral imaging and unmixing to discriminate multiple overlapping fluorescence emission profiles at once.

Zeiss Cell Observer spinning disk confocal

The Cell Observer is a hybrid instrument with five laser lines for sample excitation, 20x and 63x objectives, Yokogawa CSU-X1 spinning disk, dual Photometrics EMCCD cameras, and integrated Definite Focus system and a live cell incubator for long-term experiments.

Designed for speed, the spinning disk employs multi-point rather than single-point scanning to illuminate the sample. This allows for 4D imaging experiments where 3-dimensional Z stacks can be captured at every time point (rather than a single focal plane) to gain greater information. Simultaneous 2-channel imaging is possible using synchronised cameras and 3-channel fluorescence imaging with DIC imaging sequentially in one camera mode.

Widefield imaging

Zeiss Axioscan 7 Slide Scanner (New 2023)

Our Zeiss Axioscan 7 slide scanner combines high-speed digitisation and outstanding image quality, and a variety of imaging modes in a fully automated and easy to operate system.

Fast batch scanning of up to 100 slides in a single run at magnifications 5x, 10x, 20x, and 40x. Modalities available are colour brightfield, polarization, DIC, phase contrast and seven-channel fluorescence from UV to NIR.

Zeiss Axio Zoom.V16 (New 2023)

The Zeiss Axio Zoom.V16 is a versatile, high-performance stereo “zoom” microscope designed for a wide range of imaging applications. With its advanced optics and flexible imaging capabilities, the Axio Zoom.V16 provides exceptional resolution and clarity for both routine and specialized tasks.

The microscope features a zoom range of up to 260x total magnification, allowing users to easily switch between low- and high-magnification imaging without changing objectives. Its high-numerical-aperture 1x and 2.3x objectives and integrated illumination system provide bright, clear images with excellent contrast, even for specimens with challenging properties. Its highly sensitive colour and monochrome cameras allow for the acquisition of routine publication quality imaging.

In addition to its imaging capabilities, the Axio Zoom.V16 is also fully motorised, allowing for complex X, Y, Z, T, multi-position, tile scanning and up to four channel (DAPI, FITC, TRITC, mCherry) experiments.

This microscope also features the integrated Zeiss Apotome 3, which combines high-resolution imaging with optical sectioning capabilities. It features an innovative structured illumination technique that removes out-of-focus light, allowing for sharper, clearer confocal-like images with increased contrast and depth. The Apotome 3 is capable of imaging at multiple wavelengths making it an ideal tool for a wide range of applications including live cell imaging and 3D reconstruction.

Zeiss AxioObserver Z1

The AxioObserver is an inverted microscope with Axio Cam MRm monochrome camera, five objectives (5x to 100x) and DAPI, GFP, TRITC and Cy5 filter blocks. It is perfect for of fixed fluorescence samples. Use the AxioObserver for routine imaging automated 4-channel fluorescence and phase contrast of fixed samples.

Nikon Ti Eclipse

Versatile semi-motorised fluorescence microscope with seven objectives (2-100x) and two cameras. Use the DS-Qi1Mc monochrome camera for four channel fluorescence imaging (DAPI, FITC, TRITC and Cy5 filters) or alternatively utilise the DS-Fi1 high resolution colour camera for imaging of stained samples (e.g. H&E tissue sections). Also use this instrument for phase contrast imaging of cells in dishes. A motorised Z-drive is available for obtaining Z-stacks and NIS software can be used to perform deconvolution and produce confocal-like 3D images and extended focus images.

Olympus IX81

The IX81 is a semi motorised inverted microscope with 20x 40x, 60x and 100x objectives and filters for imaging DAPI, FITC, TRITC and Cy5. It is fitted with an Olympus DP80 dual CCD chip monochrome and colour camera running on cellSens software. Use the IX81 for acquiring images of fixed slides using fluorescence, DIC, or colour histological stains.

Olympus BX50

The BX50 is a manual upright fluorescence microscope with filters for DAPI, FITC, TRITC and Far Red imaging and has objectives ranging from 20x - 100x. Use this instrument for basic three colour fluorescence imaging of cells and tissues on slides. This instrument has the ability to carry out tile scanning via an automated stitching function and extended focal imaging of thick samples.

Image analysis

Our offline image analysis workstation is available to facility users to access our suite of software for processing and analysis of multidimensional datasets. Remote desktop connection can be used so researchers with a La Trobe VPN can access its capabilities anywhere in the world.

Bitplane Imaris - Render confocal Z stacks in 3-D, measure volumes and surface areas of objects, track paths, velocities, and displacements of moving objects in time series experiments, and analyse filament-like objects (e.g. neuronal networks) based on size, shape, and hundreds of other parameters.

Zeiss ZEN and ImageJ/Fiji - These imaging software packages offer comprehensive tools for data processing and analysis. Zeiss ZEN enables tasks like image segmentation, 3D rendering, colocalization analysis, deconvolution, and quantification. ImageJ/Fiji is an open-source software with a user-friendly interface, supporting plugins and macros for customized workflows. Coupled with a high end workstation it excels in handling large datasets, automating batch processing, and providing various image visualization options.

ORS Dragonfly and Drishti - Powerful tools for creating realistic 3D renderings of volume imaging data, ideal for publication or presentations. They enable visual showcasing of complex structures, spatial relationships, and virtual sectioning. These software packages enhance communication and presentation by generating captivating and scientifically informative 3D representations of research findings.

Agrisoft Metashape Photogrammetry Software - Simplifies the creation of 3D volumes from multiple camera angles by analysing overlapping 2D images. Metashape reconstructs geometry and texture, generating accurate 3D models with user-friendly interfaces and automated workflows. It utilizes advanced algorithms for image alignment and textured 3D mesh creation. Metashape is valuable in applications such as architecture, archaeology, and virtual reality, transforming photographs into realistic 3D volumes effortlessly.


We support researchers with equipment training and can assist with project planning, basic and advanced microscopy techniques and digital image analysis. Contact us and arrange for a tour to see what facilities are available or schedule a meeting to discuss your project.

Training and equipment bookings

To use the equipment researchers should arrange for instrument-specific training with the facility manager. Training is designed to enable users to operate the instruments competently and obtain publication quality data.Trained users can book equipment and view availability.

Complementary Capabilities

La Trobe has partnered with the Olivia Newton-John Cancer Research Institute which has complementary multiphoton imaging capabilities that can be accessed through their ACRF Centre for Imaging the Tumour Environment, as well as their VECTRA Multi-Spectral Imaging Platform.


For more information about accessing the Bioimaging Platform, please contact:

Chad Johnson
Bioimaging Platform
T: +61 3 9479 2983