Microscopy Australia

The direct quantification of programmed death-ligand 1 (PD-L1) as a biomarker for cancer diagnosis, prognosis and treatment efficacy is an unmet clinical need. Herein, we demonstrate the first report of rapid, ultrasensitive and selective electrochemical detection of PD-L1 directly in undiluted whole blood using modified gold-coated magnetic nanoparticles as "dispersible electrodes" with an ultralow detection limit of 15 attomolar and a response time of only 15 minutes.

Herein, a glucose meter-based immunosensing platform is developed that allows the quantification of procalcitonin (PCT) in whole blood samples. PCT is a biomarker for sepsis and its early detection would improve the safety of the patient, as the diagnostic process will be easier and faster. The method employs liposomes with encapsulated glucose as a signal generation tag, which are then used in a sandwich immunoassay by conjugating an antibody to the liposome. The optimal liposomes' size and concentration of encapsulated glucose is determined experimentally to be 200 nm and 27.8 mM, respectively. Upon the addition of a surfactant (Triton X-100), the glucose is released and a signal is detected with a personal glucose meter (PGM). This signal is directly proportional to the concentration of the PCT in the sample. The dynamic range of the assay developed was 0.153-15.38 nM, and could allow the detection of PCT as low as 0.15 nM. The assay showed a high selectivity toward PCT against other proteins such as C-reactive protein and human serum albumin and good reproducibility. This assay was able to quantitatively determine the amount of PCT in whole blood samples at clinically-relevant concentrations.

For this report, representatives from academic facilities in Australia and overseas that operated, or were planning to operate, electron microscopy and correlative light–electron microscopy instruments that produced large volumes of data, were interviewed. The interviews aimed to collect information on how the facilities had set up their data workflows for data capture, data transfer, data movement, data storage and overall data orchestration, which tools they used for data processing (including the supporting infrastructure), and how data and metadata were managed. Based on this survey, the report provides a review of the informatics and data-management landscape at Australian facilities, including tools, methods and procedures currently in use or commented on during interviews. Furthermore, the report proposes recommendations to the stakeholders of the Australian Characterisation Commons at Scale (ACCS) project and its Work Package 4 for tools, methods and procedures that have been considered interesting, promising or relevant to examine further over the first year of Work Package 4 (2021), and guide ACCS work packages into the future. This work was undertaken under the Australian Characterisation Commons at Scale (ACCS) project, in particular under Work Package 4: “Big-data electron and correlative microscopy from instrument to publication”.

Moving data reliably, securely and at high speed was identified as important in the report “Orchestration and management of data generated by big-data electron microscopy instruments: A Discovery report” (DOI: 10.5281/zenodo.4744876). The present report focuses on the selection of an appropriate tool for data transport, namely Globus, and its prototyping, testing and deployment at two sites. User documentation and guidelines to deploy Globus have been developed and made available online in open access. This work was undertaken under Work Package 4: “Big-data electron and correlative microscopy from instrument to publication” of the Australian Characterisation Commons at Scale (ACCS) project.

Researchers and research facilities transfer large volumes of data routinely within and between institutions and across countries and the globe. Monitoring and predicting the performance of a network as well as identifying anomalies when they arise is therefore critical. In the present report, the toolkit perfSONAR is described. perfSONAR is used by research and education organisations across the world to measure a range of network properties. Advantages of perfSONAR are briefly presented alongside recommendations on how information technology and e-research specialists, facilities and researchers may exploit and interpret information from perfSONAR. This work was undertaken under Work Package 4: “Big-data electron and correlative microscopy from instrument to publication” of the Australian Characterisation Commons at Scale (ACCS) project.

Imaging facilities underpin a growing share of modern life-science research, yet the career conditions and scholarly recognition of the Imaging Scientists in core facilities who design, deliver, and interpret imaging research remain uneven. This mismatch risks loss of expertise, reduced service quality, and weaker long-term sustainability of shared research capabilities. To provide an evidence base for practical change, we synthesise findings from two complementary international community surveys run by Global BioImaging: a “Top 5” survey on career development and job conditions (>290 responses spanning 43 countries) and an authorship/acknowledgement survey examining how publication credit is assigned for imaging-related contributions of core facility staff (>330 responses spanning 43 countries). Across both surveys, respondents consistently link limited recognition to constrained career prospects. The career survey highlights recurring bottlenecks around progression routes, job stability and attractiveness, access to professional development, and the day-to-day consequences of being perceived primarily as service providers rather than scientific partners. The authorship/acknowledgement survey documents substantial variability in credit practices across facilities, disciplines, and regions, with many respondents reporting uncertainty about expectations, difficulty initiating credit discussions, and concerns about bias and power dynamics. Taken together, the results suggest a reinforcing cycle: inconsistent credit reduces visibility and leverage for Imaging Scientists in core facilities, which in turn entrenches fragile career pathways and inhibits retention. We translate these findings into targeted, stakeholder-specific actions. Recommendations focus on defining career paths that match facility roles, aligning evaluation with the full range of facility outputs (including methods, data, software, and training), and ensuring that institutions, funders, publishers, and research teams share responsibility for fair and consistent credit.

The Microscopy Australia network – a national facility comprising 18 microscopy laboratories and approximately 270 staff across Australia – has initiated a Staff Shadowing Scheme to enable individuals throughout the network to build relationships, enhance their knowledge and skills, and to exchange ideas on training, outreach and industry support. This scheme was developed following Microscopy Australia's participation in Global Bioimaging that conducted a similar program. The program provides staff with the opportunity to visit a world-leading facility, located nationally or internationally, for a short visit (1-2 weeks) to learn from their peers and bring back knowledge, skills and training to share with their colleagues and users (i.e., trainees and clients). Since 2019, 15 staff (60% female) of all levels and classifications across eight Microscopy Australia facilities have participated in the program, visiting colleagues at labs within Australia and around the globe. The Staff Shadowing Scheme is a uniquely accessible program in that it is available to all staff regardless of level or classification (e.g., Technical Staff, Level 4; Academic Staff, Level B), and does not involve an onerous application procedure. This comprehensively broadens access to the entire Microscopy Australia cohort, enabling all staff to actively participate and benefit. The application process takes advantage of the fact that all applicants, as members of the Microscopy Australia network, already have proven skills and experience in their field and have had their application approved by their node director; the selection process can therefore focus on the nature and quality of the benefit that the scheme can provide to that particular individual and their node. For many grant schemes, new staff, mid-career and non-academic staff can be overlooked or not even qualify for grants traditionally available to the microscopy community. Likewise, staff working part-time and/or with significant time commitments outside of work can be at a disadvantage in applying for grants. As Staff Shadowing Scheme participant Dr Rhiannon Kuchel from UNSW attests, “Staff shadowing is an excellent educational tool, especially for someone like me who currently has two children (with a third on the way) and also works part time – 0.8 FTE – and who cannot always attend the rigid structure of conferences or workshops.” Rhiannon's visit to the Monash University Ramaciotti Centre for Cryo-Electron Microscopy provided her not only with hands-on experience with new techniques, but also insight into alternative training methods, and new relationships with mentors that she has carried forward in her work. Furthermore, the flexibility of the program allowed Rhiannon to determine the duration and timing of her visit so that it fit best with her work and family commitments. In the effort to continue to build and develop a vibrant microscopy community in Australia, the Staff Shadowing Scheme recognizes the importance of open, regular communication between staff at all nodes. Value is therefore placed on intangible benefits such as networking and relationship building, exposure to new processes, points of view, and perspectives on teaching, training and outreach. This approach aims to promote the development of a robust and vibrant communication infrastructure that facilitates ongoing discussion, develops familiarity, and nurtures real-time peer support between staff across the Microscopy Australia network and beyond. A Win-Win for Facilities and Users. The expanded skills and knowledge on instruments, equipment and workflows enabled by the Staff Shadowing Scheme helps to optimise the ability of Microscopy Australia to create and support cutting-edge microscopy research from the academic to the industrial sector. It has enhanced the agility of participants and their node in addressing the needs of new users across sample types and fields of inquiry. In terms of infrastructure planning and long-term roadmapping for universities and state and federal governments, the program also efficiently improves awareness across the Microscopy Australia network of emerging technologies, allowing staff to most effectively inform users and management, and advocate for/provide information supporting large-scale funding applications to keep Microscopy Australia facilities and support at the frontier of advanced microscopy and microanalysis. A) Dr Rhiannon Kuchel (UNSW, academic staff, right) with host Dr Gediminas Gervinskas at the Monash Ramaciotti Centre for Cryo-Electron Microscopy. B) Adjusting the anticontamination cold finger on the Helios G4 UX cryo-FIBSEM. Scale bar = 20 cm. Jacob Byrnes (University of Sydney, professional staff, left), with Akiko-san and Nakayama-san who provided specialist training on TEM specimen preparation during a visit to National Institute of Materials Science (NIMS), Japan.

This report outlines the engagement with global imaging communities through global networks and dedicated annual community events. The foundingGIDE community events served as a platform for engaging local and global stakeholders and facilitating collaboration and coordination of global imaging data practices. These events brought together data producers, bioimage analysts, infrastructure providers, policymakers, funders, and industry representatives to discuss challenges and future directions for imaging data interoperability. The report also highlights the project's close collaboration with Global BioImaging (GBI), leveraging its international network of research infrastructures to bridge regional gaps, identify regional data management bottlenecks, and accelerate the worldwide adoption of imaging data standards. This collaboration directly supported the coordination of three global community events. This version is pending EC approval.

In the era of big data, keeping all data or copies of data unselectively has become unrealistic or unreasonable for many research organisations. Knowing what data to keep, how to store them and for how long is essential but can be challenging. Beyond the retention and disposal of research data mandated by legislation and funding bodies, suitable practices in research data retention and disposal can play a fundamental role in making data storage sustainable and ensuring that data remain valuable, authentic and compatible with the FAIR (Findable, Accessible, Interoperable, Reusable) and CARE (Collective benefit, Authority to control, Responsibility and Ethics) data principles. They also enhance the discoverability, sharing and reuse of research data. In this report, eight recommendations are proposed to provide microscopy research facilities with guidance and foster best practices in research data retention and disposal. These recommendations are based on a survey of the facilities on their awareness and practices in data retention and disposal, and focus on key elements: 1. data retention policy; 2. data disposal (after the retention of users’ data and suitable protocol for data elimination); 3. data security and access to users’ data; 4. storage of users’ data; 5. sustainable file formats for data retention; 6. metadata collection; and 7. research data management planning. This work was undertaken under Work Package 4: “Big-data electron and correlative microscopy from instrument to publication” of the Australian Characterisation Commons at Scale (ACCS) project.

Imaging facilities underpin a growing share of modern life-science research, yet the career conditions and scholarly recognition of the Imaging Scientists in core facilities who design, deliver, and interpret imaging research remain uneven. This mismatch risks loss of expertise, reduced service quality, and weaker long-term sustainability of shared research capabilities. To provide an evidence base for practical change, we synthesise findings from two complementary international community surveys run by Global BioImaging: a “Top 5” survey on career development and job conditions (>290 responses spanning 43 countries) and an authorship/acknowledgement survey examining how publication credit is assigned for imaging-related contributions of core facility staff (>330 responses spanning 43 countries). Across both surveys, respondents consistently link limited recognition to constrained career prospects. The career survey highlights recurring bottlenecks around progression routes, job stability and attractiveness, access to professional development, and the day-to-day consequences of being perceived primarily as service providers rather than scientific partners. The authorship/acknowledgement survey documents substantial variability in credit practices across facilities, disciplines, and regions, with many respondents reporting uncertainty about expectations, difficulty initiating credit discussions, and concerns about bias and power dynamics. Taken together, the results suggest a reinforcing cycle: inconsistent credit reduces visibility and leverage for Imaging Scientists in core facilities, which in turn entrenches fragile career pathways and inhibits retention. We translate these findings into targeted, stakeholder-specific actions. Recommendations focus on defining career paths that match facility roles, aligning evaluation with the full range of facility outputs (including methods, data, software, and training), and ensuring that institutions, funders, publishers, and research teams share responsibility for fair and consistent credit.

This report outlines the engagement with global imaging communities through global networks and dedicated annual community events. The foundingGIDE community events served as a platform for engaging local and global stakeholders and facilitating collaboration and coordination of global imaging data practices. These events brought together data producers, bioimage analysts, infrastructure providers, policymakers, funders, and industry representatives to discuss challenges and future directions for imaging data interoperability. The report also highlights the project's close collaboration with Global BioImaging (GBI), leveraging its international network of research infrastructures to bridge regional gaps, identify regional data management bottlenecks, and accelerate the worldwide adoption of imaging data standards. This collaboration directly supported the coordination of three global community events. This version is pending EC approval.

Metadata play a fundamental role in making research data FAIR (findable, accessible, interoperable, reusable) by enhancing the discoverability, sharing and reuse of research data. They also increase confidence in the validity of the data by supporting research reproducibility. However, collecting metadata at microscopy facilities in a way that is sustainable and systematic has often proven challenging. The main barrier has been the inability to extract information from the various systems used by facilities (for example, for instrument booking). Many of these systems are part of the ecosystem of infrastructures provided by the universities that house facilities. In this report, five recommendations are proposed to foster best practices in metadata collection at microscopy facilities. These recommendations are based on the interviews of four university-based, microscopy research facilities. They focus on five key elements: 1. the choice of metadata schema; 2. the minimum set of metadata that every facility should at least collect; 3. the publication of metadata; 4. how facilities can collect metadata; and 5. how institutions can assist facilities in collecting metadata. This work was undertaken under Work Package 4: “Big-data electron and correlative microscopy from instrument to publication” of the Australian Characterisation Commons at Scale (ACCS) project.

Imaging facilities underpin a growing share of modern life-science research, yet the career conditions and scholarly recognition of the Imaging Scientists in core facilities who design, deliver, and interpret imaging research remain uneven. This mismatch risks loss of expertise, reduced service quality, and weaker long-term sustainability of shared research capabilities. To provide an evidence base for practical change, we synthesise findings from two complementary international community surveys run by Global BioImaging: a “Top 5” survey on career development and job conditions (>290 responses spanning 43 countries) and an authorship/acknowledgement survey examining how publication credit is assigned for imaging-related contributions of core facility staff (>330 responses spanning 43 countries). Across both surveys, respondents consistently link limited recognition to constrained career prospects. The career survey highlights recurring bottlenecks around progression routes, job stability and attractiveness, access to professional development, and the day-to-day consequences of being perceived primarily as service providers rather than scientific partners. The authorship/acknowledgement survey documents substantial variability in credit practices across facilities, disciplines, and regions, with many respondents reporting uncertainty about expectations, difficulty initiating credit discussions, and concerns about bias and power dynamics. Taken together, the results suggest a reinforcing cycle: inconsistent credit reduces visibility and leverage for Imaging Scientists in core facilities, which in turn entrenches fragile career pathways and inhibits retention. We translate these findings into targeted, stakeholder-specific actions. Recommendations focus on defining career paths that match facility roles, aligning evaluation with the full range of facility outputs (including methods, data, software, and training), and ensuring that institutions, funders, publishers, and research teams share responsibility for fair and consistent credit.

Imaging facilities underpin a growing share of modern life-science research, yet the career conditions and scholarly recognition of the Imaging Scientists in core facilities who design, deliver, and interpret imaging research remain uneven. This mismatch risks loss of expertise, reduced service quality, and weaker long-term sustainability of shared research capabilities. To provide an evidence base for practical change, we synthesise findings from two complementary international community surveys run by Global BioImaging: a “Top 5” survey on career development and job conditions (>290 responses spanning 43 countries) and an authorship/acknowledgement survey examining how publication credit is assigned for imaging-related contributions of core facility staff (>330 responses spanning 43 countries). Across both surveys, respondents consistently link limited recognition to constrained career prospects. The career survey highlights recurring bottlenecks around progression routes, job stability and attractiveness, access to professional development, and the day-to-day consequences of being perceived primarily as service providers rather than scientific partners. The authorship/acknowledgement survey documents substantial variability in credit practices across facilities, disciplines, and regions, with many respondents reporting uncertainty about expectations, difficulty initiating credit discussions, and concerns about bias and power dynamics. Taken together, the results suggest a reinforcing cycle: inconsistent credit reduces visibility and leverage for Imaging Scientists in core facilities, which in turn entrenches fragile career pathways and inhibits retention. We translate these findings into targeted, stakeholder-specific actions. Recommendations focus on defining career paths that match facility roles, aligning evaluation with the full range of facility outputs (including methods, data, software, and training), and ensuring that institutions, funders, publishers, and research teams share responsibility for fair and consistent credit.