Author Archives: Anthony Hayes

NEWS: New BIOSI Live Cell Imaging Spoke

Above: Spinning disc confocal microscope set up in the new BIOSI live cell imaging spoke

A dedicated live  cell imaging spoke has been set up in the Sir Martin Evans Building (BIOSI; E/3.15). The microscopy suite has inverted widefield, scanning and spinning disc confocal microscopes with full environmental control systems. Further information available through Pete Watson.

AJH 08/04/2022


CORE EQUIPMENT: New Zeiss Celldiscoverer 7 system

Above: Training on the Bioimaging Hub’s new Zeiss Celldiscover7 imaging system

The Bioimaging Hub has recently taken delivery of a state-of-the-art, automated  live cell imaging system to replace its old Leica SP2 confocal microscope. The Celldiscoverer7 imaging system, which was purchased via the generous support of Cardiff University’s Research Infrastructure Fund (Lead Applicant: Dr Tony Hayes), has the latest Zeiss LSM 900 confocal scan head with Airyscan 2 detector technology and is capable of multi-format, high-throughput and super-resolution analysis of a wide range of samples from cell cultures to small model organisms. The system supports photomanipulation via FRAP, FRET and related techniques and is furnished with a comprehensive Zen software package that includes modules for deconvolution and machine learning, amongst other cutting edge features. Further details of the system are available through the Bioimaging Hub’s research equipment database.


Find out more:

NEWS: Updated Covid Rules: Resumption of Hands-on Support and Training.

A huge and heartfelt thank you to all users and support staff of the Bioimaging Hub for your strict adherence to our covid security measures over the last 12 months. It has been an extremely difficult year for all of us and we have tried to manage the situation as effectively and as safely as possible, working within the security framework provided by Cardiff University and Welsh government.

In line with the latest guidance, we are pleased to now begin relaxing some of our covid security measures and to be in a position where we can reintroduce direct hands-on support and training for our microscope systems.  To facilitate this provision, it remains vitally important that users follow the new guidance protocols, as detailed below.

Before entering the Bioimaging Hub:

  • All users must familiarize themselves with current Welsh Government Coronavirus (Covid-19) Guidance and read the Bioimaging Hub’s updated Coronavirus risk assessment.
  • Users must not visit the Bioimaging Hub if they are displaying any symptoms of Covid-19; if they have been in a high risk area; or had recent contact with a covid-positive individual without confirmation of a negative test result.
  • All users are advised to make regular use of the Cardiff University covid screening service  or to utilise rapid flow testing methodology that is now widely available through the NHS and pharmacies.

Room occupancy status and technical support/training:

  • Room occupancy status has now increased to two independent users/two research bubbles per microscopy suite, up to a maximum of four people per microscopy suite in total.
  • Direct hands-on training and support for our microscope systems will now resume under social distancing rules and with PPE including face coverings.

COVID working Regulations within the Bioimaging Research Hub:

  • Users should continue to use the room booking calendars and should specify which microscope system they require in the title section of the booking request (i.e., specify user name and microscope system). Booking details here.
  • Social distancing rules remain in place within all areas of the Bioimaging Hub.
  • PPE remains mandatory including the use of face coverings in all communal areas.
  • Microscope cleaning procedures before and after use remain mandatory.
  • Histology sample drop-offs and collections should continue to be arranged via email (


AJH 28.9.2021

IN-FOCUS: Brushing Up On Your Background Knowledge.

With the dizzying pace of technological innovation and ongoing advances in microscopy and imaging, it is becoming increasingly difficult to keep abreast current developments in the field. With this in mind, we’ve rounded up some essential resources, from basic to advanced, that will keep you informed and updated.

Online magazines & journals:

Educational portals:


SPOKE EQUIPMENT: Olympus VS200 High Throughput Slide Scanning Microscope.

Above: the new Olympus VS200 high throughput slide scanning system in ECSCRI

A new, high throughput slide scanning system has recently been installed in the European Cancer Stem Cell Research Institute (ECSCRI) and is available for use as a spoke of the Bioimaging Research Hub. The equipment allows automated high-throughput scanning of histological samples via a range of image modalities, including epifluorescence. Further details of the system are available through the Hub’s equipment database. All enquiries for this system should be directed towards Mr Mark Bishop.

Further Reading:


NEWS: Reopening of the Bioimaging Research Hub: New COVID 19-Security Measures.

For the time being, use of the Bioimaging Hub is going to be a very different experience for everyone. In drawing up these guidelines we’ve taken a lead from the Welsh Government and have started with a very cautious approach that we’ll constantly review and relax where possible. For now, the guidance may seem quite stringent so please bear with us while we all adapt to this new way of working.

Access is not permitted to the Bioimaging Research Hub without (i) completing a risk assessment form that should cover all planned activities within the facility and (ii) reading all relevant supporting information (see below). A template risk assessment is available through the Bioimaging Hub’s main web pages.

Before completing the risk assessment form, all users must download and read the following documents:

Cardiff University’s COVID-19 secure organisational risk assessment

The Bioimaging Hub’s local COVID-19 security guidelines

DO NOT enter the Bioimaging Research Hub:

  • If you are SARS-Cov-2 positive or are displaying symptoms of COVID-19 infection (e.g. persistent coughing, elevated temperature, anosmia, sickness).
  • If you have been in a high-risk area or have had recent contact with confirmed SARS-CoV-2 positive individuals within the last 14 days.
  • If you have an underlying health condition and are concerned it will put you at greater risk of developing severe COVID-19 symptoms. N.B. essential work can be undertaken by Bioimaging Hub staff at a supported rate if necessary.

COVID Working Regulations within the Bioimaging Research Hub

All users of the facility:

  • MUST read the above documentation before entering the Bioimaging Research Hub.
  • MUST contact before entering the facility.You are not permitted to simply drop-in unplanned. Drop off/collection of histology samples must be arranged in advance. Researchers must knock before entering histology via E/0.08 and observe all safety directives outlined in this document. Users must complete a histology request form to specify processing preferences in advance of their visit.
  • MUST wash their hands upon entering and leaving the facility (hand wash station opposite office area). Multiple gel hand wash dispensers are also available within the microscopy suites.
  • MUST wear appropriate personal protective equipment (PPE) within the facility, including a buttoned-up lab coat and gloves (gloves are provided in all microscopy suites). Eye protection is advisable.
  • MUST clean the imaging equipment and immediate working area before and after use (cleaning instructions are available at each microscope station; alcohol spray and lab roll have been provided for this purpose).
  • MUST observe social distancing (i.e. 2 metres inter-personal space) within the Hub. The main corridor should be used by only one person at a time. While social distancing measures are in place no training is available and technical support will be provided on a remote basis via telephone (main office: 02920876611; shared office: 02922510220; histology: 02920875139).
  • MUST NOT enter the staff office area (0.14A) or histology suites (E/0.06-E/0.07). Drop off/collection of histology samples must be arranged in advance (use E/0.08).
  • MUST knock before entering any room. All microscopy suites are now single occupancy (i.e. one in, one out with at least 15 mins user-free time between bookings). The microscope booking calendars have been replaced with room booking calendars, as follows: “BIOSI – E/0.03 – Confocal/Lightsheet microscopy”, “BIOSI – E/0.04 – widefield microscopy”, “BIOSI – E/0.05 – spinning disc microscopy”. New booking instructions can be found here.
  • MUST set the room occupancy status (vacant/in use) on the door sliders of the microscopy suites before and after use.


German BioImaging recommendations for operating Imaging Core Facilities in a research environment during the SARS-CoV-2 pandemic

Leica: How to sanitize a microscope

Olympus: How to clean and sterilize your microscope

Zeiss: Cleaning and disinfecting the microscope and its optical components

IN FOCUS: Bioimaging Hub’s YouTube Channel – Rebooted.

Above: the new look Bioimaging hub YouTube channel.

With the University (and entire planet) in lockdown due to the ongoing covid 19 pandemic, now seems as good time as any to make you aware of the Bioimaging hub’s ‘rebooted’ YouTube channel, if you was not already aware of it.

A decade is a long time in imaging. Way back in 2009 we set up a YouTube channel to showcase the capability of our new, all-singing, all-dancing Leica SP2 confocal microscope. At the time, we uploaded a collection of short 3D animation sequences that highlighted some of our ongoing research applications. Fast forward eleven years. Whilst many of those early demo videos have been highly viewed (one over 20 thousand times) they’re starting to look rather dated, particularly when compared to the material that we’re now producing using our new confocal and lightsheet systems and 3D analysis software. As I say, a decade is a long time in imaging.

So, with the advent of spring, we thought it was high time we dusted down our YouTube channel and gave it an overhaul. As well as introducing lots of nice new image content from some of our latest 3D imaging systems, we felt that the channel would have a greater sense of purpose if we were to develop it into an educational resource for microscopy and bioimaging, with obvious relevance for remote learning (i.e., perfect in our current circumstances). Consequently, we have started to collate the most useful and relevant of YouTube’s microscopy-related content (webinars, tutorials, demonstrations etc), ranging from the basic principles of light microscopy to cutting-edge fluorescence-based nanoscopy techniques such as FLIM, so that they are all placed under one roof for your convenience : )

One of the things we hoped to provide our userbase was a series of video tutorials for the hub’s many microscope systems. Whilst there’s a great deal of useful training material on YouTube, in the main, it tends to be aimed at many of the high-end, turn-key imaging systems. Furthermore, not all microscopes are created equal, they each have their own peculiarities which reflect their intended function and most ‘evolve’ over time, through upgrades, to accomodate the vagaries of research. So, with this in mind, we have started to create our very own bespoke training videos for each of the hub’s microscope systems (example here).

The new training videos will supplement the standard operating procedures (SOPs) we have written for all of our imaging equipment and should provide an invaluable resource for user training and e-learning. As such, they will be embedded within the appropriate sections of the hub’s SOP repository (read more here). The online video content and their associated SOPs will be viewable at the click of a mouse button via desktop shortcuts on all of our microscope-associated PCs allowing easy access during instrument operation.

If you have time on your hands, then please pop over to YouTube and take a look at how our channel is developing (link here). It’s still work in progress but, as I say, it has the potential to be an extremely useful resource; not only for hub users, but anyone with a passing interest in microscopy and bioimaging. Constructive feedback is welcomed.


NEWS: State of the Art: An Update.

Above: Plant parts x4 . Biological pop-art on the ‘Warhols’ of the Bioimaging hub. Slide scanned images of plant tissues (various species; transverse sections) courtesy of Dr Tony Hayes, pop-art montage by Marc Isaacs.

The eagle-eyed amongst you may have noticed that the main corridor within the Bioimaging Research Hub is looking a little nattier these days. We thought it required some brightening up and so have started to adorn its walls with some nice, new A0-sized foamex prints of microscopical images that we’ve generated in-house on the Hub’s microscope systems. We’ve tried to select images that showcase the beauty of the unseen microscopic world which reflect the art in science, or ‘SciArt’ as it is known. We hope the images stimulate interest and highlight the state-of-the-art research and facilities within Cardiff School of Biosciences. No prizes for spotting the artistic influences on some of our ‘works’ : )


Further reading

Sleigh & Craske (2017) Art and science in the UK: a brief history and critical reflection. Interdisciplinary Science Reviews. 42:4, 313-330.

IN FOCUS: Plastic Fantastic – Making Pollen Models for The National Botanic Garden of Wales.

The Bioimaging research hub does a nice sideline 3D printing scale replicas of biological samples for use in science engagement and teaching. These can be made from the smallest of microscopic samples imaged via optical sectioning microscopy (i.e., confocal or lightsheet) or from large anatomical samples imaged via 3D photogrammetry or from 3D scanning techniques. I’ve posted a few blogs on this site in the past describing 3D pollen models that we’ve made for various research groups within Cardiff University (e.g. for the ‘Footprints in time’ and ‘PharmaBees’ projects) and for a growing number of external organisations within the UK and abroad (e.g. the Met office, the Smithsonian institute etc).

Recently, we were approached by the National Botanic Gardens of Wales (NBGW) to generate 3D models of twenty different species of pollen grains identified in honey by Dr Natasha De Vere’s research group for their science outreach and engagement programme. Natasha is the head of science at the NBGW and is using cutting edge DNA bar coding technology to understand pollinator foraging preferences. This research is providing amazing insights into the selective range of plant species that important pollinating insects such as bees visit when foraging (you can read more about this fascinating work here and in the reference below).

To generate the 3D prints we first needed pollen samples from each of the respective plant species – you’d be forgiven if you thought the National Botanic Gardens could provide these ‘off the shelf’ : ) Coming from a zoological background, my botany field skills are best described as rudimentary. So, equipped with my smartphone, a plant identifier app that I downloaded from the Google Play store, and some zip-lock sample bags, I embarked upon a ‘Pokemon-go style’ palynological quest (‘gotta catch ’em all’) that took me to the local parks, woodlands, river embankments, country lanes and coastlines and even garden centres of South Wales.

After some effort, I managed to identify and collect all of the pollen species on the wish list. I then began to image representative grains from each species using the Hub’s Zeiss LSM880 Airyscan confocal microscope. Individual grains were optically sectioned through their volume, 3D reconstructed and then output in a file format for 3D printing on our Ultimaker 3D printer (method described in reference below).

The finished 3D pollen models are shown in the photograph above – each model is approximately 15cm in diameter (i.e., enlarged by a factor of approximately x400 relative to the original pollen grain). The models will be on display at the Growing the Future stand at this year’s Royal Welsh show (20-23rd July, 2019) and also at the Pollinator festival at the National Botanical Gardens of Wales (24-26th August, 2019).


Further Reading

Hawkins, J., de Vere, N., Griffith, A., Ford, C.R., Allainguillaume, J., Hegarty, M.J., Baillie, L., Adams-Groom, B. (2015) Using DNA metabarcoding to identify the floral composition of honey: a new tool for investigating honey bee foraging preferences. PLoS ONE 10 (8): e0134735.

Perry, I., Szeto, J-Y., Isaacs, M.D., Gealy, E.C., Rose, R., Scofield, S., Watson, P.D., Hayes, A.J. (2017) Production of 3D printed scale models from microscope volume datasets for use in STEM educationEMS Engineering Science Journal1 (1): 002.


Sample collection and preparation, confocal microscopy, 3D reconstruction and file conversions by Dr Tony Hayes; 3D printing by Dr Pete Watson; Photography by Marc Isaacs.

CORE EQUIPMENT: Widefield Microscope Upgrades.

The Bioimaging Hub’s conventional widefield microscope systems have recently received some performance upgrades. Details of upgrades below:

N.B. All of the above systems are now networked via 1GB desktop switches. Up-to-date standard operating procedures and risk assessments for each system are available through the Bioimaging hub’s online SOP repository via their desktop folders (‘Read me before use’). See a member of staff for further details.