“You’re obviously not a scientist”

Exactly what you want to be told by the photographer, whilst wearing your graduation regalia, about to accept your Master’s degree in Physics…

Fortunately I’ve grown enough in confidence over the course of my degree (with especial thanks to to my formidable female physics supervisors in Auckland who I need to write and thank) to immediately retort “Actually sir, I’m a female medical physicist”.

This blog aims to document my journey since graduation on the NHS Scientist Training Programme to become a medical physicist. (It might help form a part of my competencies too…)



Radiotherapy Patient Pathway

Having spent 3 months in the radiotherapy physics department, I finally got the opportunity today to spend some time with the radiographers, scanning, planning and treating patients. This blog post will hopefully illustrate my understanding of the pathway that patients go through for their radiotherapy treatment as well as some reflections I have had over the last few months.


Immobilisation is necessary in radiotherapy to ensure that the treatment position is replicable from planning to treatment fraction to fraction. Immobilisation is most effective when the outer contour of the body matches the internal structure for example in head and neck treatments. In lower body treatments such as prostate or cervix, the internal anatomy is a bit squishier and less related to the outside anatomy and so different techniques such as bladder filling and rectal voiding are used to increase repeatibility.

The below photo is of a head and neck mask. This shell is created using a thermoplastic warmed in a water bath until soft and pliable. The patient lies on the treatment couch and the mask is applied over their face and attached to the couch with screws at the side. It hardens as it cools and forms a shell that will be used over the course of their treatment. Some centres make a mask for all their radiographers when they join the Trust to increase their empathy for the patient experience which I think is a brilliant idea!

Head and neck radiotherapy mask ( https://www.bbc.co.uk/news/uk-england-devon-21622782 )

Today we had an elderly patient for palliative care with no immobilisation specified by the referring consultant. After consulting with the superintendent radiographer, it was determined that immobilisation was definitely necessary considering the position of her tumour and its relation to her bony anatomy. However she refused to have a head and neck mask made, opting instead for a chin strap. This is a less reliable way of setting her up for treatment but the pros and cons were described to her and at the end of the day we have to respect the patient’s choice. It was really inspiring to watch the kindness with which she was treated by the radiographers, and in fact the kindness with which the radiographers treated all of their patients.

It’s very easy to forget in our Physics ivory tower (or rather windowless basement!) that everything we do concerns real people who are not equivalent to the perspex phantoms we do tests on! And there’s no point creating a technique or procedure that provides clinically better results if patients aren’t going to tolerate the treatment.

Planning CT

The planning CT is performed with the patient in the treatment position that they will be in during treatment. This means their immobilisation and comfort aids are used here. These include things such as the head and neck mask as discussed above but also things like knee supports, breast boards with handles that enable you to rest the arms above the head and neck cushions. All of these are designed for the comfort of the patient whilst lying on the treatment bed as well as repeatibility of the treatment position.

Patients also receive their setup tattoos during the planning CT. The lasers in the CT room are used to project points of intersection onto the patient which are marked with felt tip crosses. These crosses are then covered with radio opaque wire crosses during the CT scan so that they can be seen on the CT image. Breast patients also have any surgery scars outlined with radio opaque wire so it is visible on the CT scan as clinicians sometimes like to ensure that the entire scar is included within the radiation field jaw edges.

After the CT scan is complete, the centre of these felt tip crosses will be permanently tattooed onto the patient using ink and a needle by the radiographers. These tattoos enable the radiographers to set up a patient in the treatment room each day. They are so small I was quite impressed that the radiographers could find them so easily on the patients during treatment!


This part of the patient pathway is not seen by the patient but definitely seen by the physicists and dosimetrists!


The patient’s CT scan and information is imported into the treatment planning system. The appropriate protocol as specified by their referring clinician is attached to their CT scan and their CT scan is checked. The CT scans are checked for the date, time, number of slices and image quality to provide assurance that the correct patient scan has been imported and that all of the data has been transferred correctly (e.g. no network errors). At this point, planners will then fuse any other imaging patients have had with this CT scan. MRI images are good for soft tissue contrast but we need the electron density information from the CT scan to do our treatment planning. By fusing the image sets, we have both sets of information at our fingertips for outlining body structures and clinical target volumes as well as planning.


After importing and any fusing, the clinicians outline the gross target volume (the tumour) and the clinical target volume (which contains a margin added in for non-imageable microscopic spread of the disease). It’s then passed back to the physics & dosimetry team for outlining of the organs at risk and planning target volume growth. The planning target volume is the clinical target volume with margins added on for geometrical uncertainties in the treatment process. These will then be approved by the clinician and it’s time to plan!


The aim of radiotherapy is to irradiate the target volume whilst minimising the dose to the healthy tissue and this is what the planning is all about. Using different sized fields, beam angles, wedges, multi-leaf collimators and segments, the planners will optimise the dose distribution such that the prescription dose to the target volume is achieved whilst minimising dose to the healthy tissue & the organs at risk in the area. In an ideal world, 100% of the dose would be given to the tumour and 0% to the healthy tissue but unfortunately this is not achievable.

The quality of the plan is assessed in a variety of ways, including looking at the dose volume histograms (i.e. how much dose is the organ receiving per percentage volume of the organ), looking at the dose distributions in different CT slices and checking the organ at risk tolerances, e.g. we want no more than 50% of the bladder to receive no more than 50 Gy. These tolerances are taken from historical data, observations & trials.


After the planning is complete and checked by an entirely independent physicist, the clinician must sign off on the plan and the plan must be checked by the radiographers. There is a weekly multidisciplinary team meeting for each treatment site in which each patient in the planning part of the patient pathway is discussed and any issues can be brought up and resolved.


On the first day of a patient’s treatment, a radiographer will set aside some time to explain what to expect during treatment in terms of appointments, side effects and answering any questions they might have.

Some patients have specific preparation to undertake before every treatment. For example prostate patients will often be asked to have an enema, empty their bladder and drink 3 cups of water in the hour before their treatment. This means they have to turn up for their appointment up to an hour and a half before their allotted treatment time. Other patients have no specific preparations as such, it is very site dependent.

Imaging protocols during treatment differ between treatment sites and patients. Some sites are imaged with CBCT before every treatment and others are only imaged in the first few fractions. For example in head and neck, we expect the treatment position to be extremely reproducible each fraction due to the use of the mask however I saw a patient who was being imaged for every treatment because the differences between the set-up detailed on the set-up sheet and the set-up that was achieved on the treatment couch when aligning the lasers to the tattoos & mask crosses were greater than expected. On the bed imaging ensures the patient is in the position they are expected to be in when their treatment is delivered.

Breast cancer patient on treatment couch. (The best picture I could find without using a manufacturer’s one of a beautiful woman wearing a bra posing on a machine…..) https://www.astro.org/News-and-Publications/News-and-Media-Center/News-Releases/2018/ASTRO-issues-clinical-guideline-for-whole-breast-r

The radiographers were truly amazing in their care and patience despite a very high patient throughput. Each patient was treated with such dignity and respect (as should be the bare minimum of course!) and no one was hurried along despite the time pressures in play.

It was also interesting to see how the decisions that physics make affect the radiographers. For example when picking the isocentre for a treatment, I’ve been told to always pick a whole number of centimetres for the shift to the tattoos to make it easier for the radiographers when setting up a patient. I had suggested that surely the radiographers have enough mental maths to cope with adding 2 numbers but now having spent time with them doing patient setup I’d like to rescind all previous comments! They have more than enough to focus on without having to add non-integer numbers!


Physicists are vital for safe, efficacious radiotherapy treatment. However radiographers are the ones who have to deal with the consequences of the decisions that physicists make when we pick odd beam angles or strange patient shifts or decide to match or not match certain machines etc.

This day was really valuable in reminding me the importance of patient centred treatment and I’d thoroughly recommend that physicists get sent along to spend some time with radiographers in pre-treatment and on- treatment on a reasonably regular basis to be reminded of the importance of patient centred healthcare and multidisciplinary teamwork.


Radiotherapy has a lot of abbreviations and today I’ve had to relearn some of the most annoying of them all:

TCP= Tumour Control Probability

NTCP= Normal Tissue Complication Probability

For a good radiotherapy treatment we want TCP>= 0.5 and NTCP <=0.05


ART*- less of an art, more of a science.

*(Adaptive Radiotherapy)

People are the worst, right? Humans have their own internal biases, their own ways of doing things, their own subjectivity and their own distractions.

So why don’t we just automate all treatment planning? This was certainly the attitude that I took at before beginning this placement in radiotherapy.  It turns out that it’s not as simple as I expected…. What a surprise!

My first impressions of treatment planning were that it is definitely more of an art form than a science. Contouring organs is not in the skill set gained from 5 years + physics higher education. But once you learn where the rectum starts and ends (ischial┬átuberosities anyone?) and get over the fact that the bowel seems to occupy some people’s entire abdominal cavity, you can be safe in the knowledge that you’ve tried your hardest and that someone with years of study of anatomy behind them will (hopefully) be giving it the once-over.


Auto segmentation and autocontouring organs at risk (OARs) using AI is now a thing and is even used clinically in 2 hospitals in Finland for prostate plans. MVision (https://mvision.ai/) is a cloud based system which sends anonymised patient scans (CT and/or MRI) outside the hospital and then uses its neural net trained from patient data from 6 partners in Finland, Estonia and Singapore to produce OAR outlines based on ESTRO guidelines. The prostate model is now CE marked for clinical use in Europe. Hosting it on the cloud means that it can be easily updated as the model learns more however does beg the question how to commission a system that is constantly evolving?

(I also have a lot of questions in terms of consent and personal data but we’ll save those for another day).

So say we do use autocontouring within the treatment planning pathway and no longer have to spend minutes (experienced people) or hours (me trying to contour bowel) tediously drawing around bits of anatomy. What can we do with this freed up time!? And more importantly, how can we get even more free time to work on novel techniques? What else could we automate?!

Automated Treatment Planning

Physicists and dosimetrists have already automated treatment planning to an extent. In each department there is usually a “recipe book” to follow for specific sites and dose prescriptions such that the planner has a starting point for beam angles etc rather than starting from scratch. But entire automation of the treatment planning seems like a pipe dream? Or is it?

Dose Prediction Knowledge based planning

Unsurprisingly, knowledge based planning uses prior experience to either predict an achievable dose or to give a better starting point for the planner to use. There are 2 separate methods:

Atlas based

Atlas based knowledge based planning selects the closest matching patients to build a predictive DVH model for the patient in question. This DVH however is only for the regions of interest (ROI) delineated, not other tissue so there’s no avoidance of hotspots etc, and no spatial information.

Model based

Model based knowledge based planning builds a model to predict the dose to individual voxels within the patient’s image.

Both of these methods mean that created plans can only be as good as the training data and that created plans can be clinically acceptable but not necessarily optimal. One advantage of this method is that the model is trained on patient anatomy and not treatment technique so transferring between treatment techniques should not be too difficult however the model must be trained for each clinical site.

As a tool for checking, predicting achievable dosimetry, training new staff, improving human planning and QA-ing clinical trials, this technique holds a lot of promise.

Protocol Based Automatic Iterative Optimisation (PB-AIO)

PB-AIO is an automated iterative adjustment of objective and constraints. A user defined template with required clinical objectives (hard constraints) is used to start with. AI systems can simulate the reasoning behaviour of a human planner, using “fuzzy logic” to convert trial and error of expert human planners to binary “IF-THEN” logic statements.

This leads to a reduction in inter-operator variability. Harder dose constraints are met at a similar level to human planning but the PB-AIO meets the less tight constraints more admirably than the humans. This is probably because a human operator’s focus is upon meeting the harder, tighter constraints.

This tool could be used to improve plan quality but not remove optimisation. Some experienced planners perform better than PB-AIO in particular cases.

Multicriteria Optimisation (MCO)

The pareto optimal solution in multicriteria optimisation is a solution that can’t be improved without degrading at least one other objective. Each pareto optimal solution is not necessarily clinical optimal but the clinically optimal plan will be a pareto optimal solution. There are an infinite number of pareto optimal solutions.

A posteriori

Multiple plans are generated, each is a pareto optimal solution. Each is optimised to an extent where it can’t be improved upon without affecting other criterion. Each plan is a pareto optimal solution. An infinite number of plans could be generated but it is recommended N+1 plans are optimised where N= no. of objectives.

The human planner then reviews the N+1 plans produced and picks the clinically optimal solution.

These plans are optimised in fluence space which does not necessarily directly translate to machine parameter optimisation. The dosimetric difference is unlikely to be large but it can be especially in the case of very complex MLC movement patterns.

A priori

In “A priori MCO”, a single pareto optimal plan is generated by using a treatment site specific wishlist with assigned priorities and hard constraints. This multidisciplinary wishlist of criteria is made, reviewing recently treated patients and clinical protocols. Iterative improves of the wishlist will have to occur. These type of plans however do not allow for patient specific adaptation (e.g. prosthetic hip).

In 2 prospective studies, the a priori automatically generated plan was picked 32/33 and 29/30 times which shows strong promise!

Final thoughts

Automated treatment planning reduces variability between plans and could be used to prevent human bias and subjectivity when comparing different treatment techniques in a treatment planning study or when making the decision to support novel techniques. It could also be very valuable in using for “plan of the day” adaptive radiotherapy.

I don’t think all the humans are going to be out of a job just yet however. Humans perform better in unusual cases, and how do you get that experience? Years of planning!

Also who is going to make the plans to feed into the systems to train them? Who will help set wishlists for MCO? Who is going to pick the best plans? Who is going to check the plans are physically deliverable?

The final thing to note is that radiotherapy is done to improve a patient’s life. Our jobs are all about the patient coming first. Whether the radiotherapy treatment is palliative or curative, a clinician has taken the view that radiotherapy is a valuable part of the patient’s treatment. The above planning techniques are all linked to DVH-like metrics rather than patient outcomes so for radiotherapy to advance to being truly personalised, there is still some work to do.

10/10 can recommend a read of this review article if you’re interested: https://www.birpublications.org/doi/10.1259/bjr.20180270

What even is an x-ray?

I’ve always been taught the electromagnetic spectrum goes (in song form)

Radiowaves, Microwaves, Infrared… Radiation, Visible light, Ultraviolet, X-rays, Gamma rays.

The assumption being that the higher the note sung (the later in the song), the higher the energy, the shorter the wavelength u.s.w.

Therefore why are we calling my LINAC friends x-ray units?! Their energy is way higher than a conventional diagnostic x-ray and way higher than the gamma rays required in say pair production of an electron and positron. Where has the system failed? What is the energy distinction between x-rays and gamma rays?!

Spoiler alert: There isn’t one…

X-rays are defined by the Australian Radiation Protection and Nuclear Safety Agency (ARPANSA) as being produced when electrons strike a target or when electrons rearrange within an atom. Whereas Gamma rays originate from the settling process of an excited nucleus of a radionuclide after it undergoes radioactive decay.

And so method of production is the distinction between x-rays and gamma rays rather than energy.

In a linear accelerator, the photons are produced by accelerating electrons into a heavy metal target (e.g. Tungsten), therefore they are in fact x-ray units despite the colossal energies being worked with!

Electronic spirit levels

I’m more than happy with how an “analogue” spirit level works. A cylinder with a slight upward curve in the middle (or a larger diameter in the middle) is incompletely filled with a spirit. This leaves a bubble which travels to the centre of the cylinder when on a flat surface. When on a slight level the bubble travels to not be in the centre. Additional lines can be drawn on the tube to represent inclinations of 45 degrees etc.

So how can a digital spirit level possibly know whether it’s on an inclination or not!? Answer: witchcraft*.

No one at work could give me a satisfactory answer but fortunately my friend the internet gave a guide on how to build my own electronic spirit level ( http://embedded-lab.com/blog/build-a-digital-spirit-level-using-a-sca610-accelerometer/). For this build you will need: an accelerometer, a microcontroller (like a microprocesser but with RAM, ROM etc) and some other electronic things and also some knowledge of programming and electronics.

But the most important component is the accelerometer!

*or science. Sometimes the same thing in all honesty.


There are lots of ways to make an accelerometer. In essence you need an accelerative force to create a change in your device that you can measure. One way of doing this is using the piezoelectric effect to create a voltage within a crystal that can then be measured. Another is to have a micro capacitor with a fixed plate and one that can move. As the accelerative force moves the moveable one, the capacitance between them changes which can be measured and converted to voltage.

A digital spirit level uses an accelerometer that can sense accelerations of -g to g. At -g, the spirit level reads -90 degrees and at g, reads 90 degrees. Between these two values the angles are interpolated from the voltage et voila, a digital spirit level!

A/N: Learning about how all this worked is my favourite kind of science. Simple concepts that when put together create something that was beyond your comprehension before you started reading about it! P.S. This is related to medical physics due to how we use spirit levels in testing radiotherapy treatment units and the recommendations of IPEM 81.

Patients come first!

Today we’re scheduled to spend a whole day on radiotherapy machine quality assurance (QA), performing the monthly checks on a particular machine to ensure that we are operating within the approved procedures with which we’re allowed to carry out radiotherapy. These checks include mechanical checks of the couch positioning and isocentres (laser, mechanical, radiation), dosimetric checks such as looking at the treatment beam profile and image guided checks including checking that the cone beam CT images are of high enough quality to be clinically acceptable.

Anything out of tolerance will require a permit, signed by the head of department to enable the machine to continue in clinical use. This permit will include a justification of continuing to use the machine and an assessment of the clinical effect. Anything that requires immediate attention will cause the machine to be pulled out of clinical use immediately.

This morning’s radiographer QA checks have pulled up an action serious enough that treatments cannot be given on this machine until the action has been fixed. This means patients scheduled to be treated on this machine have to be transferred to other machines due to the time critical nature of administering radiotherapy (where patients have been following instructions for bladder filling etc). This also means that Physics QA is delayed until the department is back to having all machines being operational. As with everything in healthcare science, the clinical needs of the patients come first!