Category Archives: equipment

EQUIPMENT: New 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

AJH

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:

AJH

EQUIPMENT: New Zeiss PALM MicroBeam laser micro-dissector.

palm

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.

EQUIPMENT: New spinning disc confocal system for live cell imaging.

spinning-disc

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.

AJH

 Further reading:

NEWS: Picoquant FLIM module installed on new confocal.

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.

AJH

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EQUIPMENT: New multi-spectral real time 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. All enquiries for this system should be directed towards Dr Amit Jathoul.

AJH

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EQUIPMENT: New Bitplane Imaris workstation for advanced 3D/4D image processing.

Imaris Screenshot

Image: Screenshot of the new Imaris software showing a surface-rendered model of an insect’s compound eye.

The Bioimaging Research Hub has recently purchased Bitplane Imaris software for Cell Biologists, together with a high-end PC workstation, via generous funding from the Research Infrastructure Fund (lead applicant: Dr Walter Dewitte). The software provides advanced  processing options for confocal and multi-photon 3D/4D datasets and includes the following modules: Measurement Pro, Imaris Track, Imaris Cell, Imaris Coloc, Imaris XT and Imaris Vantage. Further details of the system are available via our equipment database.

AJH

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EQUIPMENT: New, state-of-the-art, confocal laser scanning microscope with super-resolution capability.

DSC_0459

Image: The old and the new: The new Zeiss LSM 880 Airyscan confocal system (right) adjacent to the old Leica TCS SP2 confocal (left) (BIOSI 2; E/0.03)

The BIOSI Bioimaging facility has recently expanded its imaging toolbox with a new, state-of-the-art confocal microscope system, that was purchased through generous funding by the Research Infrastructure Fund (Lead Applicant: Dr Walter Dewitte). The system, a top-of-the-range Zeiss LSM 880 upright confocal microscope, features the advanced Airyscan super-resolution detection module which provides a 1.7x gain in resolution in all three dimensions compared to conventional confocal optics. The system also supports advanced fluorescence techniques including FCS (fluorescence correlation microscopy) and FLIM (fluorescence lifetime imaging (FLIM) – the FLIM module will be installed during the first week of December. Further details here.

AJH

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