Advanced Microscopy and Immunochemistry

The Florey Advanced Microscopy and Immunochemistry Service (FAMIS), a joint Florey and University of Melbourne facility, offers a collection of state-of-the-art light microscopy equipment and image processing tools.

FAMIS supports in-house scientists and visitors in using light microscopy methods for their research.

We also regularly organise in-house and international courses to teach basic and advanced light microscopy methods. 

Hours: 8.30am to 4.30pm Monday to Friday

Facility staff

Carolina Chavez (PhD) 

Mikhail Trubetskov (PhD)









FAMIS provides access to:

  • Two confocal microscopes (Zeiss LSM 780 and Leica TCS SP8)
  • Live cell imaging capabilities on Leica SP8 with incubator, perfusion system and electrical stimulator
  • Two stereology workstations (brightfield and fluorescence and Stereo Investigator)
  • One Neurolucida workstation (brightfield and fluorescence also including Stereo Investigator)
  • Server-based deconvolution (Huygens core)
  • Server-based analysis tools (Imaris, Amira, FIJI)
  • Offline analysis workstation Stereo Investigator and Neurolucida Lite

All users of microscopy equipment need to be trained or demonstrate competence before access is permitted. Contact the platform to arrange training and platform induction.


The facility supports in-house scientists and visitors in using light microscopy methods for their research. We also regularly organise workshops and courses to teach basic and advanced light microscopy as well as analysis methods.

The experienced microscopy team can assist users throughout the entire process of microscopic imaging: planning of an experiment, sample preparation, selection and usage of the microscope, image processing and visualisation, data transfer and storage.

We are passionate about quantitative imaging and we provide both state-of-the-art equipment and know-how to quantify any aspect of your sample, from volume of structures of interest to number of neurons, synaptic contacts, neurite lengths and connectivity to co-localisation and dynamic processes in live cells. We provide server-based deconvolution using Huygens deconvolution software (SVI) to increase resolution and contrast, decrease noise and correct artefacts such as chromatic shifts, crosstalk and object movement.



To use the microscopes within facility you will need an account for our booking system and arrange for a training session on the piece of equipment you would like to work with.  Training session lengths depend on the microscope and application, contact for further information.



Analysis server (Imaris, Amira, FIJI)

Please email for login details.

PRICING - Please email as each user will have different requirements and support levels

If you have any questions please contact staff:


The facility provides access to three software packages to facilitate quantitative analysis of microscopic data sets. These programs are installed on a dedicated analysis server which can be used remotely. Please email for login details.

Imaris F1 package for neuroscientists -

3D/4D visualization and analysis methods with object detection and Filament Tracer for automated detection of neurons including spines and other filamentous structures in 2D/3D or 4D datasets, measurements, object tracking, plotting, group comparisons with statistical tests and two-way interface for customization in Matlab, Java or Python.

Amira (FEI) 3D visualization and analysis software -

Amira provides a comprehensive array of tools for the flexible and accurate analysis of time series data of cellular processes. It enables researchers to perform dedicated segmentation workflows on their intra- and intercellular images and apply powerful automated object tracking solution.

  • Single cell tracking
  • Single particle tracking
  • Filament tracing and editing

FIJI (imageJ)

Fiji is a free image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.


Image processing and analysis programs


· Zeiss Zen Lite 

· Leica LASX Lite 

· Imaris (Bitplane) 

· Amira (FEI) 

· FIJI (ImageJ) 


Microscopy reading and tutorials:

· Leica-Microsystems Basics in Microscopy

· Education in Microscopy & Digital Imaging (Zeiss) 

· Olympus Microscopy basics and tutorials 

· Microscopy primer (all about microscopy, fluorescence etc)

· EAMNET (Teaching modules on microscopy techniques, teaching courses and downloads of microscopy related software packages) 

· Microscopyu (Nikon)  

The AMIF presently manages 10 state of the art microscope systems from industry leading imaging companies. Several workstations for image analysis are provided.

Head to SVI for more information on scientific volume imaging


The dorsal raphe nucleus in a mouse

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