Tag Archives: Covid-19

Barcoding bees

Every jar of honey I prepare carries a square 20mm label that identifies the apiary, batch, bucket and the date on which is was jarred. The customer can scan it to find out about local honey … and hopefully order some more.

The label looks a bit like this:

Scan me!

This is a QR code.

You’ll find QR codes on many packaged goods in the supermarket, on bus stop adverts, on … well, just about anything these days.  QR codes were first used in 1994 and are now ubiquitous.

QR is an abbreviation of quick response.

It’s a machine-readable two-dimensional barcode that is used to provide information about the thing it’s attached to.

QR codes contain positional and informational content. In the image above the three corners containing large squares allow the orientation to be unambiguously determined.

Within the mass of other, much smaller, black and white squares are several alignment points, an indication of the encoding 1 and the ‘information payload’. 

Large QR codes can contain more information and more error correction (so they can be read if damaged 2 ). Conversely, small QR codes contain reduced amounts of information and less error correction, but can still be used to uniquely identify individual things in a machine-readable manner.

A barcoded bee and barcode diagram.

And those ‘things’ include bees.

I am not a number 3

I had intended to write a post on how pathogens alter honey bee behaviour. This has been known about in general terms for some time, but only at a rather crude or generic level. 

To understand behavioural changes in more detail you need to do two things:

  • observe bees in a ‘natural setting’ (or at least as natural as can be achieved in the laboratory)
  • record hundreds or thousands of interactions between bees to be able to discriminate between normal and abnormal behaviour. 

And that isn’t easy because they tend to all look rather similar.

Lots of bees

How many of the bees above are engaging in trophallaxis?

Does the number increase or decrease over the next five minutes? What about the next hour?

And is it the same bees now and in an hour?

And what is trophallaxis anyway? 

I’ll address the last point after describing the technology that enables these questions to be answered.

And, since it’s the same technology that has been used to monitor the behavioural changes induced by pathogens, I’ll have to return to that topic in a week or two. 

Gene Robinson and colleagues from the University of Illinois at Urbana–Champaign have developed a system for barcoding bees to enable their unique identification 4.

Not just a few bees … not just a couple of dozen bees … every bee in the colony.

Though, admittedly, the colonies are rather small 😉

Each barcode carries a unique number, readable by computer, that can be tracked in real time.

So, unlike Patrick McGoohan, these bees are a number.


The scientists designed a derivative of the QR code that could be printed small enough to be superglued to the thorax of a worker bee. They termed these mini-QR-like codes bCodes 5. The information content of a bCode was limited by its size and the reference points it had to carry that allowed the orientation of the bee to be determined.

In total the bCode could carry 27 bits of data. Eleven bits (each essentially on or off, indicated by a black or white square) encoded the identification number, allowing up to 2048 bees to be uniquely numbered. The remaining 16 bits were the error-correction parity bits that had to be present to ensure the number could be accurately decoded.

If you’re thinking ahead you’ll realise that the maximum number of bees they could therefore simultaneously study was 2048. That’s about 1/25th of a very strong colony at the peak of the season, or the number of bees covering both sides of a two-thirds full frame of sealed brood.

It’s enough bees to start a one frame nucleus hive, which will behave like a mini-colony 6 and, in due course, expand to be a much larger colony.

And if you’re thinking a long way ahead you’ll realise the every barcode must be affixed to each bee in the same orientation. How otherwise would you determine whether the bees were head to head or abdomen to abdomen?

Labelling bees

This is the easy bit.

Each bCode was 2.1mm square and weighed 0.6mg i.e. ~0.7% of the weight of a worker bee. Honey bees can ‘carry’ a lot more than that. When they gorge themselves before swarming they ingest ~35mg of honey. 

The bCode therefore should not be an encumbrance to the bee (and they confirmed this in an exhaustive series of control studies).

A single frame of sealed brood was incubated and the bees labelled within a few hours of emergence. Typically, two batches of ~700 bees each were labelled from a single frame for a single experiment.

Each bee was anaesthetised by chilling on ice, the bCode glued in place (remember … in the same orientation on every bee) and the bee allowed to recover.

Labelling a single bee took 1-2 minutes.

Labelling 1400 bees takes several people a long time.

I said it was easy.

I didn’t say it was interesting.

Smile for the camera

I’ve not yet discussed the goal of the study that needed barcoded bees. It’s not really important while I’m focusing on the technology. Suffice to say the scientists wanted to observe bees under near natural conditions.

Which means a free-flying colony, on a frame of comb … in the dark.

Free-flying because caged bees do not behave normally.

On a frame of comb because they were interested in the interactions between bees under conditions in which they would normally interact.

And in the dark because that’s what it’s like inside a beehive (and it’s one of the features that scout bees favour when selecting a site for a swarm).

Camera and hive setup.

The scientists used an observation hive with a difference. It had an entrance to allow the bees to fly and forage freely and it contained a single sided, single frame. In front of the frame was a sheet of glass separated by 8mm from the comb. This prevented the bees from clambering over each other, which would have obscured the bCodes 7. Behind the frame was an 850nm infrared lamp to increase contrast, and the front was illuminated by several additional infrared lamps.

Bees cannot see light in the infrared range, so they were effectively in the dark.

The camera used (an Allied Vision Prosilica GX6600 … not your typical point and shoot) recorded ~29MP images every second. A typical experiment would involve the collection of about a million images occupying 4-6 terabytes of hard drive space 8.

The recorded images were processed to determine the temporal location of every bee with a visible (and readable) bCode. This was a computationally interesting challenge and involved discarding some data – e.g. barcodes that moved faster than a bee can walk or barcodes that fell to the bottom of the hive and remained motionless for days (i.e. dead bees). About 6% of the data was discarded during this post-processing analysis.


Which finally gets us to the point where we can discuss trophallaxis. 

Honey bees and other social insects engage it trophallaxis.

It involves two insects touching each other with their antennae while orally transferring liquid food. It occurs more frequently than would be required for just feeding and it has been implicated in communication and disease transmission

bCoded bees and trophallaxis

So, if you are interested in trophallaxis, how do you determine which bees are engaging in it, and which are just facing each other head to head?

In the image above the two bees in the center horizontally of the insert 9 are engaged in trophallaxis. The others are not, even those immediately adjacent to the central pair.

Image processing to detect trophallaxis – head detection.

This required yet more image processing. The image was screened for bees that were close enough together and aligned correctly. An additional set of custom computer-vision algorithms then determined the shape, size, position and orientation of the bees’ heads. To be defined as trophallaxis the heads had to be connected by thin shapes representing the antennae or proboscis.

And when I say the image … I mean all million or so images.

Bursty behaviour

And after all that the authors weren’t really interested in trophallaxis at all.

What they were really interested in was the characteristics of interactions in social networks, and the consequences of those interactions.

This is getting us into network theory which is defined as “Well out of my depth”

Transmission of things in a network depends upon interactions between the individuals in the network.

Think about pheromones, or honey, or email … or Covid-19.

It’s only when two individuals interact that these can be transmitted between the individuals. And the interaction of individuals is often characterised by intermittency and unpredictable timing. 

Those in the know – and I repeat, I’m not one of them – call this burstiness. 

If you model the spread of ‘stuff’ (information, food, disease) through a bursty human communication network it is slower than expected.

Is this an inherent characteristic of bursty networks?

Are there real bursty networks that can be analysed.

By analysing trophallaxis Gene Robinson and colleagues showed that honey bee communication networks were also bursty (i.e. displayed intermittent and unpredictable interactions), closely resembling those seen in humans.

However, since they had identified every trophallaxis interaction over several days they could follow the spread of ‘stuff’ through the interacting network.

By simply overlaying the real records of millions of interactions over several days of an entire functional community with an event transmitted during trophallaxis they could investigate this spread..  

For example, “infect” (in silico) bee 874 in the initial second and follow the spread of the “infection” from bee to bee through the real network of known interactions.

In doing this they showed that in a real bursty network, interactions between honey bees spread ‘stuff’ about 50% faster than in randomised reference networks. 

Why isn’t entirely clear (certainly to me 10, and seemingly to the authors as well). One obvious possibility is that the topology of the network i.e. the contacts within it, are not random. Another is that the temporal features of a bursty network influence real transmission events. 

Scientists involved in network theory will have to work this out, but at least they have a tractable model to test things on …

… and at a time when some remain in lockdown, when others think it’s all a hoax, when social distancing is 2m 11, when some are wearing masks and when prior infection may not provide protective immunity anyway, you’ll appreciate that ‘how stuff spreads’ through a network is actually rather important.

Stay safe


Time to deploy!

It’s early April. The weather is finally warming up and the crocus and snowdrops are long gone. Depending where you are in the UK the OSR may start flowering in the next fortnight or so.

All of which means that colonies should be expanding well and will probably start thinking of swarming in the next few weeks.

So … just like any normal season really.

Except that the Covid-19 pandemic means that this season is anything but normal.

Keep on keeping on

The clearest guidelines for good beekeeping practice during the Covid-19 pandemic are on the National Bee Unit website. Essentially it is business as usual with the caveats that good hygiene (personal and apiary) and social distancing must be maintained.

Specifically this excludes inspections with more than one person at the hive. Mentoring, at least the really useful “hands-on” mentoring, cannot continue.

A veil is no protection against aerosolised SARS-CoV-2. Don’t even think about risking it.

This means that there will be a lot of new beekeepers (those that acquired bees this year or late last season) inspecting colonies without the benefit of help and advice immediately to hand.

Mistakes will be made.

Queen cells will be missed.

Colonies will swarm 1.

Queen cells

Queen cells …

It’s too early to say whether the current restrictions on society are going to be sufficient to reduce coronavirus spread in the community. It’s clear that some are still flouting the rules. More stringent measures may be needed. For beekeepers who keep their bees in out apiaries, the most concerning would be a very restrictive movement ban. In China and (probably) Italy these measures proved to be effective, although damaging to beekeeping, so the precedent is established.

Many hives and apiaries are already poorly managed 2. I would expect that additional coronavirus-related restrictions would only increase the numbers of colonies allowed to “fend for themselves” over the coming season.

Which brings me back to swarming.


The final point of advice on the NBU website is specifically about swarms and swarm management:

You should use husbandry techniques to minimise swarming. If you have to respond to collect a swarm you need to ensure that you use the guidelines on social distancing when collecting the swarm. If that is not possible, then the swarm then should not be collected. Therefore trying to prevent swarms is the best approach. 

Collecting swarms can be difficult enough at the best of times 3. And cutouts of established colonies are even worse.

In normal years I always prefer to reduce the swarms I might be called to 4 by setting out bait hives.

Swarm recently arrived in a bait hive with a planting tray roof …

Let the bees do the work.

Then all you need do is collect them once they’re all neatly tucked away in a hive busy drawing comb.

This year, with who-knows-what happening next, I’ll be setting out more bait hives than usual with the expectation that there may well be additional swarms.

If they’re successful I’ll have more bees to deal with when the ‘old normal’ finally returns. If they remain unused then all I’ve lost is the tiny investment of time made in April to set them out.

Not just any dark box

I’ve discussed the well-established ‘design features’ of a good bait hive several times in the past. Fortunately the requirements are easy to meet.

  • A dark empty void with a volume of about 40 litres.
  • A solid floor.
  • A small entrance of about 10cm2, at the bottom of the void, ideally south facing.
  • Something that ‘smells’ of bees.
  • Ideally located well above the ground.

I ignore the last of these. I’d prefer to have an easy-to-reach bait hive to collect rather than struggle at the top of a ladder. If I wanted to do some vertically-challenging beekeeping I’d go out and collect more swarms 😉

So, ignoring the final point, what I’ve described is the nearly perfect bait hive.

Those paying attention at the back will realise that it’s also a nearly perfect description of a single brood National hive.

How convenient 🙂

All of my bait hives are either single National brood boxes or two stacked National supers. The box does need a solid floor and a crownboard and roof. If you haven’t got a spare solid floor you can easily build them from Correx 5 for a few pence.

Inside ...

Bait hive floor

Alternatively, simply tape down a piece of cardboard or Correx over the mesh of an open mesh floor 6. In some ways this is preferable as it’s convenient to be able to monitor Varroa levels after a swarm arrives.

Do not be tempted to use a nuc box as a bait hive. You can easily fit a small swarm into a brood box, but a really big prime swarm will not fit in a 5 frame nuc box.

Big swarms are better 🙂 7

More to the point, bees are genetically programmed to search for a void of about 40 litres, so many swarms will simply overlook your nuc box for a more spacious nest site.

What’s in the box?

No, this has nothing to do with Gwyneth Paltrow in Se7en.

How do you make your bait hive even more desirable to the scout bees that search out nest sites? How do you encourage those scouts to advertise the bait hive to their sister scouts? Remember, that it’s only once the scouts have reached a democratic consensus on the best local nest site that the bivouacked swarm will move in.

The brood box ideally smells of bees. If it has previously held a colony that might be sufficient.

Bait hive ...

Bait hive …

However, a single old, dark brood frame pushed up against one sidewall not only provides the necessary ‘bee smell’, but also gives the incoming queen space to immediately start laying 8.

You can increase the attractiveness by adding a couple of drops of lemongrass oil to the top bar of this dark brood frame. Lemongrass oil mimics the pheromone produced from the Nasonov gland. There’s no need to Splash it all over … just a drop or two, replenished every couple of weeks. I usually soak the end of a cotton bud, and lay it along the frame top bar.

Lemongrass oil and cotton bud

The old brood frame must not contain stores – you’re trying to attract scouts, not robbers.

The incoming swarm will be keen to draw fresh comb for the queen to lay up with eggs. Whilst you can simply provide some frames and foundation, this has two disadvantages:

  • the vertical sheets of foundation effectively make the void appear smaller than it really is. The scout bees estimate the volume by walking around the perimeter and taking short internal flights. If they crash into a sheet of foundation during the flight the box will seem smaller than it really is.
  • foundation costs money. Quite significant amounts of money if you are setting out half a dozen bait hives. Sure, they’ll use it but – like putting a new carpet into a house you’re trying to sell – it’s certainly not the deal-clincher.

No foundation for that

Rather than filling the box with about £10 worth of premium foundation, a far better idea is to use foundationless frames. Importantly these provide the bees somewhere to draw new comb whilst not reducing the apparent volume of the brood box.

If you’ve not used foundationless frames before, a bait hive is an ideal time to give them a try.

There are two things you should be on the lookout for. The first is that the bait hive is horizontal 9. Bees draw comb vertically down, so if the hive slopes there’s a good chance the comb will be drawn at an angle to the top bar.

And that’s just plain irritating … because it’s avoidable with a bit of care.

Bamboo foundationless frames

Bamboo foundationless frames

The second thing is that the colony needs checking as it starts to draw comb. Sometimes the bees ignore your helpful lollipop stick ‘starter strips’ and decide to go their own way, filling the box with cross comb.

Beautiful … but equally irritating 🙂

Final touches

For real convenience I leave my bait hives ready to move from wherever they’re sited to my quarantine apiary (I’ll deal with both these points in a second).

Wedge the frames together with a small block of expanded cell foam so that they cannot shift about when the hive is moved.

Foam block ...

Foam block …

And then strap the whole lot up tight so you can move them easily and quickly when you need to.

Bait hive location and relocation

Swarms tend to move relatively modest distances from the hives they, er, swarmed from. The initial bivouac is usually just a few metres away. The scout bees survey a wide area, certainly well over a mile in all directions. However, several studies have shown that bees generally choose to move a few hundred yards or less.

It’s therefore a good idea to have a bait hive that sort of distance from your own apiaries.

Or even tucked away in the corner of the apiary itself.

I’ve had bees move out of one box, bivouac a short distance away and then occupy a bait hive on a hive stand adjacent to the original hive.

It’s probably definitely poor form to position a bait hive a short distance from someone else’s apiary 😉

But there’s nothing stopping you putting a bait hive at the bottom of your garden or – whilst maintaining social distancing of course – in the gardens of friends and family.

If you want to move a swarm that has occupied a bait hive the usual “less than 3 feet or more than 3 miles” rule applies unless you move them within the first couple of days of arrival. Swarms have an interesting plasticity of spatial memory (which deserves a post of its own) but will have fully reorientated to the bait hive location within a few days.

So, if the bait hive is in grandma’s garden, but grandma doesn’t want bees permanently, you need to move them promptly … or move them over three miles.

Or move grandma 😉

Lucky dip

Swarms, whether dropped into a skep or attracted to a bait hive, are a bit of a lucky dip. Now and again you get a fantastic prize, but often it’s of rather low value.

The good ones are great, but even the poor ones can be used.

But there’s an additional benefit … every one that arrives self-propelled in your bait hive is one less reported to the BBKA “swarm line” or that becomes an unwelcome tenant in the eaves of a house 10.

As long as they’re healthy, even a bad tempered colony headed by a queen with a poor laying pattern, can usefully be united to create a stronger colony to exploit late season nectar.

Varroa treatment of a new swarm in a bait hive…

But they must be healthy.

Swarms will potentially have a reasonably high mite count and will probably need treating within a week of arrival in the bait hive 11. Dribbled or vaporised oxalic acid/Api-Bioxal would be my choice; it’s effective when the colony has no sealed brood 12 and requires a single treatment.

But swarms can bring even more unwelcome payloads than Varroa mites. If you keep bees in an area where foulbroods are established be extremely careful to confirm that the arriving swarm isn’t affected. This requires letting the colony rear brood while isolated in a quarantine apiary.

How do you know whether there are problems with foulbroods in your area? Register your apiary on Beebase and talk to your local bee inspector.

My bait hives go out in the second or third week of April … but I’m on the cool east coast of Scotland. When I lived in the Midlands they used to be deployed in early April. If you’re in the balmy south they should probably be out already 13.

What are you waiting for 😉 ?