Category Archives: equipment

IN FOCUS: Making the Most of Your Microscope.

Above: A selection of stage plate inserts 3D printed by the Bioimaging Research Hub – links to resources in blog article below.

Hands up if your microscope is badly in need of upgrade or repair but your budget won’t stretch that far? Maybe a new focusing knob to replace the one that just broke off in your hand, or perhaps a new stage plate adapter, reflector cube or filter holder to increase your imaging options? Perhaps a C-mount or smartphone adaptor to give one of your old microscopes a new lease of life? Or even a sample holder or chamber for a bespoke imaging application? What the heck, let’s think big eh? How about a completely new modular microscope system with tile scanning capabilities?

Way too expensive, eh?… Well, imagine for a moment that you could just click a button (or a few buttons, at least) and make it so. If you haven’t yet realised, I’m talking about 3D printing in light microscopy and the life sciences – the subject of a very interesting paper that I recently came across  – see below.

It’s safe to say that 3D printing is changing the way we do things in microscopy, now permitting low-cost upgrade, repair, or customisation of microscopes like never before. There are now a huge selection of 3D printable resources available through websites such as NIH3D, Thingiverse etc that can be used to modify your microscope system or to generate scientific apparatus or labware for upstream sample processing and preparation procedures.

So, to save you trawling through the 3D printing sites in order to identify the most useful designs to meet your histology and imaging needs we’ve done it for you and have curated a list of 3D printable resources which we hope you you’ll find useful (below).

AJH 25/05/2023

Further Reading


3D printable resources for histology and light microscopy. Information collated by Dr Tony Hayes, Bioimaging Research Hub, School of Biosciences, Cardiff University, Wales, UK.

 Sample processing

Sample staining

Sample storage and archiving

 Sample presentation

Microscope: Complete builds

Microscope: Maintenance

Microscope: Phone adapters (a selection)

Microscope: Stands (a selection)

Microscope: Components (generic)

Microscope: Olympus-specific

 Microscopes: Leica-specific

Microscopes: Zeiss-specific

 Microscopes: Nikon-specific

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:

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:


SPOKE EQUIPMENT: X-Clarity Tissue Clearing System.

One of the problems associated with imaging fluorescence in large biological samples is the obscuring effects of light scatter. Traditionally this has meant physically sectioning the material into optically-thin slices in order to visualise microscopic structure.  With the advent of new volumetric imaging techniques, e.g.  lightsheet microscopy, there is increasing demand for procedures that allow deeper interrogation of biological tissues. With this in mind, an innovative clearing system has recently been purchased through generous donations to the European Cancer Stem Cell Research Institute (ECSCRI). The equipment, which will be housed in ECSCRI lab space, allows large, intact histological samples to be rendered transparent for fluorescent labelling and 3D visualisation by confocal and lightsheet microscopy.

The X-Clarity tissue clearing system is designed to simplify, standardise and accelerate tissue clearing using the CLARITY technique (an acronymn for Clear Lipid-exchanged Acrylamide-hydridized Rigid Imaging/Immunostaining/in situ-hybridization-compatible Tissue hYdrogel). In the technique,  preserved tissues are first embedded in a hydrogel support matrix. The lipids are then extracted via electrophoresis to create a stable, optically transparent tissue-hydrogel hybrid that permits immunofluorescent labelling and downstream 3D imaging.

The new equipment and associated reagents will have wide relevance to many areas of research in Cardiff,  including deep visualisation of breast cancer tumours by Professor Matt Smalley’s research group  using  the Bioimaging Hub’s new lightsheet system. You can see a video here that shows the power of the  CLARITY technique for high resolution 3D visualisation  of tissue and organ structure.

Further Reading


SPOKE EQUIPMENT: New Ultimaker 3 ‘Extended’ 3D Printer.

Above: The new Ultimaker ‘Extended’ 3D printer building a stage insert for a novel microscope system.

The Bioimaging Research Hub has recently purchased an Ultimaker 3 ‘Extended’ professional 3D printer. The printer will allow users to 3D print bespoke pieces of scientific equipment or generate scale models  of microscopic samples for use in their research as well as for teaching, outreach and engagement activities (examples can be  found  here and here).

The 3D printer utilises FDM (Fused Deposition Modelling) printing technology and has a range of advanced features allowing the fabrication of professional quality, high resolution 3D prints. The printer can print in two different colours or a single colour in addition to a dissolvable PVA support scaffold, thus allowing complex overhanging structures to be printed at high fidelity whilst significantly reducing  finishing time.

The printer has a large build volume (215 x 215 x 300mm), supports a range of materials (nylon, PLA, ABS, CPE and PVA) and has a print resolution of 20-200 microns.  The printer is wi-fi enabled with an internal webcam so that users can remotely monitor the progress of their 3D prints.

Further details of the equipment are available through our equipment database.

Further reading:


SPOKE EQUIPMENT: Zeiss PALM MicroBeam Laser Micro-dissector.


Above: ‘Cutting-edge’ equipment: the Zeiss PALM MicroBeam laser micro-dissector located at the European Cancer Stem Cell Research Institute (ECSCRI)

A Zeiss PALM MicroBeam laser micro-dissector system is now available as a spoke of the Bioimaging Research Hub. The equipment, which is located at the European Cancer Stem Cell Research Institute (ECSCRI),  allows isolation of DNA, RNA and protein from laser micro-dissected samples from both histological sections (paraffin wax or cryo) and live cells. Further details of the system are available through our equipment database. All enquiries for this system should be directed towards Mr Mark Bishop.


CORE EQUIPMENT: New Spinning Disc Confocal System for Live Cell Imaging.


Above: The new spinning disc confocal system

The old electron microscopy darkroom (BIOSI 2; E/0.05) within the Bioimaging Research Hub has recently been refurbished as a live cell imaging suite via generous support from BIOSI. It now houses a spinning disc confocal system for  fast, live cell imaging applications. The system is based around an Olympus IX71 inverted microscope, kindly provided by Dr Pete Watson, which has been upgraded, via ISSF funding, with a Crest Optics X-Light V2 confocal head, a Cairn Research tri-line laser bank (405nm, 488nm, 561nm) and a Hamamatsu ORCA Flash 4 sCMOS digital camera with M-View Gemini image splitter.  The system is fully integrated via Molecular Devices MetaMorph software and boasts a 40″ 4k display.  The system will expand the Hub’s imaging toolbox, enabling high speed, multi-position, multi-colour 3D/4D image acquisition. Support systems for live cell imaging (i.e. gas and incubation) are also available within the facility. Further details of this system are available through our equipment database.


IN-FOCUS: Bigging it up: 3D printing to change the shape of microscopy.

3d pollen

Virtual to reality: a surface-rendered digital image of a single pollen grain generated by confocal microscopy (left) is 3D printed into a 2000x scale replica model (centre & right).

Imagine being able to generate a highly accurate, solid scale replica of the sample that you are visualising down the microscope; a perfectly-rendered pollen grain, or blood cell, or microscopic organism, but big enough to hold and examine in your hand.  It would allow much better 3D conceptualisation of the sample, particularly for blind or visually-impaired individuals, and would have enormous utility in teaching and in engagement activities, and what researcher wouldn’t want a tangible, physical embodiment of their research to help explain their work (and impress their colleagues) at scientific meetings? Sounds like the stuff of science fiction doesn’t it? Well, not any more. Thanks to 3D printing technology (and the help of Dr Simon Scofield‘s lab) we have started taking volume datasets from the confocal microscope out of the virtual world and making them a reality. If you would be interested in generating a highly accurate scale model of your favourite biological sample (or would simply like to handle a giant pollen grain!) then please feel free to get in touch.


 Further reading:

CORE EQUIPMENT: PicoQuant FLIM upgrade for the Zeiss LSM880 Airyscan Confocal Microscope.

FLIM demo

Image: Dr Pete Watson (left) gets to grips with the new Picoquant FLIM module. Dr Volker Buschmann of PicoQuant (right) provides expert advice.

Our new Zeiss LSM880 Airyscan confocal system has now been upgraded with the PicoQuant FLIM module for Fluorescence Lifetime IMaging. This module provides an additional two lasers (picosecond pulsed 440nm and 485nm diodes) and utilizes the Zeiss BiG.2 GaAsP detector to allow time-correlated single photon counting (TCSPC). The FLIM module is run through Picoquant Symphotime software, which integrates seamlessly with the Zeiss Zen Black confocal software.


Find out more:

SPOKE EQUIPMENT: New Multi-Spectral In Vivo Imaging system.

Dr Amit Jathoul and Professor Jim Murray (BIOSI) have recently obtained generous funding from the Wellcome Trust to purchase a real-time, multi-spectral in vivo imaging system from Biospace Lab. The PhotonIMAGER allows bioluminescence/fluorescence imaging at a wide range of scales from cells, tissues and organs to entire complex organisms, thereby bridging the gap  from single cell to whole organism imaging. Further details of the system are available through the research equipment database.


Find out more:
Further reading: