Data collections can be seen on:!/q=%20/class=collection/p=1/group=AMMRF/

Instruments where data are captured/transferred from:

Olympus FV1000 confocal microscope, Olympus Cell R live cell microscope and Olympus Total Internal Reflection microscope

Software is available at:

Software categories:


Integration collection records

party records and activity records which may be external to an institution

Project Members:

Miles Apperley (Project Sponsor,

Simon Ringer (Project Board,

ANDS Contact:

Alan Glixman (

Project Status:


Microscopy Data Capture and Deposit

The University of Sydney

Collaborator(s): Australian Centre for Microscopy and Microanalysis (ACMM), Australian Microscopy and Microanalysis Research Facility (AMMRF)

Project Description:

Experiments conducted using high-end microscopy instruments currently record information in multiple dimensions, such as 3D and 4D, often with multiple detectors. Research data collections are therefore increasing in size as microscopy techniques evolve, often resulting in extremely large images that are difficult to manage using current infrastructure and systems. Images also often require post-acquisition processing steps where the research data moves between analytical platforms, which can be situated in different sites.

These issues have created data management requirements for a growing community of microscopists, necessitating development of infrastructure to transfer experimental research data from instruments to a research data repository. Automated capture and storage of associated metadata is also critical, in order to enable research data to be discoverable and accessible by the data producer in addition to other researchers. An existing NeAT Australian Microscopy and Microanalysis Research Facility (AMMRF) PfC project implemented by Intersect developed a data management system (DMS) for microscopy research data from X-ray microCT and Local Electrode Atom Probe (LEAPĀ®) platforms.

The research data repository supporting this system is based at the Australian Centre for Microscopy and Microanalysis (ACMM). The information collected is being made available to all AMMRF researchers and others who are granted access permissions by the data producers. The University of Sydney DC2E Microscopy data capture project will complement the DMS project by catering for additional light microscopy instruments, extending the scope for the repository that the current project is developing.

The DMS tool developed during the project is now able to manage data generated by the Olympus FV1000 confocal microscope, Olympus Cell R live cell microscope and Olympus Total Internal Reflection microscope.
Ongoing engagement and communication with user communities, monitoring of the DMS use and general decision-making over the DMS will be co-ordinated by the ACMM Director and monitored across the entire AMMRF through the AMMRF eResearch committee. The AMMRF is a national facility, and as such whilst the DMS will initially be deployed at the Sydney node of the AMMRF, this will be available for assessment by other nodes and facilities.

High Level Software Functionality:

- Data capture: it has an API that allows developers to customise the data capture process, which in DMS terminology includes the ability to copy data from the instrument into a data repository and attach metadata to it during this process.

- Basic data management: It allows users to browse storage locaitons (instruments, ftp servers, even local drive) to copy data to and from different places. Data copy between two locations (when not the user's PC) is actually treated as third-party copy, so no user intervention is required.

- Data advertisement: the metadata catalogue has been configured with RIF-CS, ANDS, so users can advertise collections in the Research Data Australia federated catalogue.

- Support for the download of data from the DMS when the user is on both hospital networks and University networks.