Project Homepage:

Instruments where data are captured/transferred from:

biomedical instruments

Project Members:

Anitha Kannan (Project Manager,

Kim Linton (Senior Business Analyst,

Sindhu Emilda (Lead Developer,

ANDS Contact:

Xiaobin Shen (

Project Status:


Comprehensive Data Management for Microscopy Research Datasets

Monash University

Project Description:

Monash Micro Imaging (MMI) is a microscopy and imaging research support facility located at Monash University and provides access to a range of biomedical instruments and services including:
• Optical and fluorescence microscopy
• Confocal microscopy
• Live cell imaging
• Transmission electron microscopy
• Scanning electron microscopy
• Cryo methods for tissue preparation
• Digital imaging and image analysis

Currently, the metadata captured on any imaging instrument provides only instrument-specific information in instrument and manufacturer-specific data formats. Additionally, in microscopy, there is no available system or software platform that allows digital capture of the experimental sample-specific metadata. Currently, the information identifying, describing, and qualifying the analysed sample is present only in the researcher’s hand-written notes or memory. The scientific data, once stored in a data and metadata repository, is only identifiable by its file name and a link between this filename and the experimental metadata is left to chance. This makes the use and in particular the re-use of experimental raw data and refined microscopy datasets difficult, and in some cases, impossible. While detailed here in the context of microscopy, the underlying issue is obviously common to any experimental data set lacking adequate annotation.

The purpose of this project was to provide software tools to support the organisation of microscopy research datasets, particularly microscopy imaging data along with the associated annotation and metadata, both instrumental and experimental, into institutional repositories and into other discovery services including Australian Research Data Commons (ARDC).

The solution delivered incorporates an existing platform for visualisation, management and analysis of biological microscope images – OMERO, which has been widely adopted within the international microscopy community. This platform establishes a concept for mandatory annotation of digital experimental data that will maximise the use, re-use and distribution of scientific raw data and experimental information within the research community. Additional functionality developed as a plug-in for OMERO provides the researchers with the ability to specify data license and generate files that allow microscopy data collections to be made publicly available for search and harvest by Research Data Australia.

Overall, the solution provided by the Comprehensive Data Management for Microscopy Research Datasets project has enhanced the MMI microscopy imaging data management process. This in turn supports research in areas that benefit from access to these microscopy data collections.

Through ANDS funding and support of the OMERO-based solution, microscopy research data has been transformed in the following ways:

From unmanaged to managed, as evident by:
• Ease and speed in the management of microscopy imaging data and metadata;
• Allowing, and in some cases mandating, storage of additional further descriptive ‘metadata’ against each data collection;
• Storage of data sets on an institutional based managed and backed up data store (LaRDS).

From disconnected to connected, as seen by:
• Research data being semantically linked to its researchers and grants via registration to the ANDS Research Data Australia database.
• Enabling the linkage of publications written by researchers with the actual research data.

From invisible to findable, as shown by:
• Provision of a simple interface to allow registration of Data Collections with the ANDS Research Data Australia database.

From single-use to reusable, as demonstrated by:
• Ability for users to define multiple levels of sharing of Data Collections to make them accessible for researchers to search, view and download data where such access has been permitted.

Overall, the Comprehensive Data Management for Microscopy Research Datasets solution provides MMI with the ability to manage large microscopy data collections, promoting more effective research based on exploiting existing collections, creation and storage of new collections and better collaborative research opportunities.

Data Type:

microscopy image: - Optical and fluorescence microscopy - Confocal microscopy - Live cell imaging - Transmission electron microscopy - Scanning electron microscopy - Cryo methods for tissue preparation - Digital imaging and image analysis

High Level Software Functionality:

OMERO was selected for its data management and sharing capability which includes:
- Importing Files
- Organising Files
- Viewing Files
- Analysing Files
- Exporting Files
- Sharing Files through groups

Further development will be completed in order to extend on the sharing capability by creating an interface from the OMERO client to Research Data Australia.