Above: Maximum intensity projections of actin stress fibres (red) and microtubules (green) of an endothelial cell imaged on a Zeiss LSM880 Airyscan confocal microscope. Z-stacks were sampled via: A. Conventional confocal optics (5 minutes scan time) B. Airyscan Fast – 0.5x Nyquist sampling (30 seconds scan time) C. Airyscan Fast – 1.5x Nyquist sampling (1 minute scan time) D. Airyscan Fast – 2x Nyquist sampling (5 mins scan time).

Through generous support of Cardiff School of Biosciences, the Bioimaging Research Hub has recently upgraded its Zeiss LSM880 Airyscan confocal system for fast image acquisition via the Zeiss Fast module upgrade. The Airyscan system allows imaging at a resolution  1.7x that of conventional confocal optics (find out more here) and the new fast  upgrade provides a 4x speed enhancement with improved signal to noise ratio. The technique uses  beam shaping optics to elongate the excitation spot along the y axis so that it simultaneously covers four lines in a single scan. This parallelisation approach, whilst increasing acquisition speeds by a factor of four, allows high pixel dwell times to be maintained resulting in high a signal to noise ratio.  You can read more about the technique below or, if you would prefer,  kick back and watch this explanatory webinar courtesy of Zeiss.

Further reading

Huff, J. (2016) The Fast mode for Zeiss LSM880 with AIryscan: high-speed confocal imaging with super-resolution and improved signal to noise. Nature Methods 13: 10.1038/nmeth.f.398.

AJH

Above: Guess which animal species. Some of the 3D printed brains for the Brain Games 2018 event.

How many of you can tell the difference between the brains of, say, a human, a black rhino and a Sloth bear? Nope, me neither, but apparently, when it comes to brains, it’s not just size that counts (see below). This conundrum is one of the many fab activities on offer this weekend at the National Museum of Wales annual Brain Games event funded by the Society for Neuroscience and highlighting the range of brain-related research undertaken at Cardiff University.

In the build up to the event, our very own Pete Watson in collaboration with Emma Lane (PHRMY) has been 3D printing brains from a wide variety of animal species, including human, on the Bioimaging Hub’s Ultimaker 3 extended dual colour 3D printer. However, just to make things a little more challenging, they’ve generated two sets of 3D prints: the first set of brains are anatomically correct scale models, the other set have all been 3D printed at an identical size – and it’s up to you, dear reader, to determine which brain belongs to what animal species.

Above are a small selection of the 3D printed brains that will be on display at the National Museum this Sunday, including a glow in the dark brain from…well, that would be telling wouldn’t it?!

AJH

Further information:

• Brain Games official webpage (Facebook)
• Scientific American. Fact or Fiction: When it comes to intelligence, does brain size matter?

You may remember one of our blogs from 2015 about a virtual histology slidebox  in development by the Bioimaging Research Hub? If not, link here.  Well, I’m very pleased to report that we’ve made considerable progress since then.

The resource has now been moved from its humble beginnings (a Rasberry Pi/raid drive set-up) to a new PC server based within the Bioimaging Research Hub. The database has also been developed significantly through mySQL which allows efficient management of the image metadata via a web interface, allowing the images to be sorted, filtered and navigated online.  

The image collection has now been expanded significantly; thus, in addition to the original histopathology collection (which contained approximately 400 digitised sections of normal and pathological tissues), we now have two new additional sections on cell biology and parasitology.

The cell biology section contains both zoomable/navigable images and interactive 3D models of intracellular structure, including major organelles, cytoplasmic inclusions and cytoskeletal components. These were all generated from confocal fluorescence datasets imaged using our Zeiss LSM880 airyscan confocal system and rendered in 3D via Bitplane Imaris. The parasitology section, meanwhile, contains over 200 new zoomable/navigable  images of various parasitic species,  organised phylogenetically for easy reference and sorting. As before, these images were generated using our Navigator slide scanning system.

So far, the database has been trialed for small group anatomy teaching, as well as for a number of BIOSI practical classes including Research Techniques (#BIT002), Advanced Research Techniques (#BI4002) and the Identifying Organelles (#BI2231) module. It is also utilized extensively for outreach and engagement activities within the Bioimaging hub to showcase our research capabilities.

As the database is a bespoke system that has been developed in house, there are no costly subscriptions involved. We are also uniquely positioned within the Bioimaging Hub to expand and develop the database according to the needs of the user.  It therefore has enormous potential as a centralized repository for microscopical image data for teaching, research and outreach/engagement purposes.

We are planning to add additional sections on plant biology and entomology  and we would welcome collaboration with any BIOSI staff who have access to the relevant slide resources and would be happy to  help in curating these collections.

Ultimately, the plan is to find a permanent home for the virtual microscopy database as part of the new e-learning and assessment facility (eLEAF) within BIOSI.

Please take a look at the database here: http://vmdb.bios.cf.ac.uk/. Any feedback (+/-) would be welcome.

Thanks again to all involved so far.

AJH

Above:  Not to be sneezed at: 3D pollen prints for the Met Office (grass, green; oak, yellow and birch, blue).

Disclaimer: If you suffer from hayfever then please avoid spending too long on this page – it may be detrimental to your health!

I bet you didn’t know that one in five people  suffer from hayfever and that 95% of pollen sufferers are allergic to grass pollen in the UK alone? Well neither did I until I visited the Met Office’s pollen forecast website. 

It seems that some of the worst offenders are pollen grains from grass, oak and birch which play havoc with the mucous membranes during the pollen season, causing sneezing, nasal congestion, itchy eyes and triggering asthma in susceptible individuals (and to make matters worse,  these conditions are exacerbated  by drinking alcohol – so no respite there!)

Having read some of our previous blogs (here and here), the Met Office recently asked the Bioimaging Hub if we would generate 3D printed models of some of the worse culprits  (shown above) for their outreach & engagement programme to help promote awareness of hayfever. 

The 3D prints were generated from surface-rendered confocal microscope volume datasets with help from BIOSI 3D printing. We’ve used the technique to generate physical models of a variety of microscopic samples ranging in size from subcellular organelles to whole developmental organisms. If you’re interested, then further details of the methodology are available below.

AJH

Further reading:

• 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 education. EMS Engineering Science Journal. 1 (1): 002.

Above: ‘Crowning glory’: Webcam shots (1-12) showing stages in the process of 3D printing a giant human molar (left) and the resultant 3D print with support scaffold removed (central and right).

The other day we were presented with a problem: was it possible to generate a 3D model of a human tooth that could be used for dental teaching and outreach purposes? The only thing was, the individual concerned didn’t specify the desired size. With a build volume of 215 x 215 x 300mm and printing resolution of 20-200 microns, our new Ultimaker 3 Extended 3D printer can print BIG, so what better application to put the new instrument through its paces! After a quick search on Thingiverse.com, we downloaded a stereolithography (.stl) file of a human molar tooth segmented from computed tomography (thanks to fvillena). We decided to print it as big as we could, but using the lowest print resolution and lowest level of infill. The results, shown above, are quite impressive – it took approximately 24 hours to print the tooth (crown-side down, root-side up) and with the support scaffold removed resulted in a 3D model approximately 300mm in height – about the same size as tooth from an adult T-Rex!! I suppose we can now be accused of (wait for it…) getting a bit long in the tooth!

AJH

Further reading:

• 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 education. EMS Engineering Science Journal. 1 (1): 002.

Above: Tripping the light fantastic: the new Zeiss Lightsheet Z.1 fluorescence microscope.

A state-of-the-art, Zeiss Lightsheet Z.1 system has recently been installed within the Bioimaging Research Hub (BIOSI 2; E/0.03). The single plane illumination microscope (SPIM) , purchased through generous funding by Cardiff University’s Research Infrastructure Fund (Lead applicant: Dr Pete Watson), allows fast and gentle multi-channel 3D/4D fluorescence imaging at the sub-cellular level. The system offers the potential of whole organ imaging of fixed cleared samples and can provide an unprecedented insight into developmental processes occurring in live model organisms such as Arabadopsis thaliana (Thale Cress), Danio rerio (Zebrafish) and Drosophila melanogaster (Fruit fly), and in vitro organoid at a high spatio-temporal resolution. Further information about this system is available via the Bioimaging Hub equipment database.

Webinars:

• Zeiss Webinar: In Vivo and Cleared Tissue Imaging with Light Sheet Microscopy
• Zeiss Microscopy How to: Mount cleared samples in Lightsheet Z.1

Further reading:

• Zeiss website: Zeiss Lightsheet Z.1
• Zeiss website: Sample Preparation for Light Sheet Microscopy