cell tracking

Publication bias. Grant bias.

All academics writing grants will tell you this: if you want to be successful when applying to a thematic research grant call, you must tick all of the boxes.

Now, imagine that you are a physicist, expert in quantum mechanics. A major funding opportunity arises, exactly matching your interest and track record. That is great news. Obviously you will apply. One difficulty however is that, amongst other things, the call specifies that your project should lead to the “development of highly sensitive approaches enabling the simultaneous determination of the exact position and momentum of a particle“.

At that point, you have three options. The first one is to write a super sexy proposal that somehow ignores the Heisenberg principle. The second option is to write a proposal that addresses the other priorities, but fudges around that particular specification, maybe even alluding to the Heisenberg principle. The third option is to renounce.

The first option is dishonest. The second option is more honest, but, in effect, is not so different from the third: your project is unlikely to get funded if you do not stick to the requirements of the call, as noted above. The third option demonstrates integrity but won’t help you with your career, nor, more importantly with doing any research at all.

And so, you have it. Thematic grant calls that ask for impossible achievements, nourished by publication bias and hype, further contribute to distortion of science.

OK, I’ll confess: I have had a major grant rejected. It was a beautiful EU project (whether BREXIT is partly to blame I do not know). It was not about quantum mechanics but about cell tracking. The call asked for simultaneous “detection of single cells and cell morphologies” and “non-invasive whole body monitoring (magnetic, optical) in large animals” which is just about as impossible as breaking the Heisenberg principle, albeit for less fundamental reasons. We went for option 2. We had a super strong team.

Gold nanorods to shine light on the fate of implanted stem cells


Joan Comenge

This is a guest post by Joan Comenge

Our work regarding the use of gold nanorods as contrast agents for photoacoustic tracking of stem cells has been just published (or here*). You can find all the technical details of the work there, so I will try to explain here the work for the readers who are not very familiar with our field.

It is important to have the appropriate tools to evaluate safety and efficacy of regenerative medicine therapies in preclinical models before they can be translated to the clinics. This is why there is an interest in developing new imaging technologies that enable real time cell tracking with improved sensitivity and/or resolution. This work is our contribution to this field.

To distinguish therapeutic cells from the patient’s own cells (or here from the mouse’s own cell),  the therapeutic cells have to be labelled before they are implanted. It is well known, that biological tissue is more transparent to some regions of the light spectrum than others. This fact is very easy to try at home (or at your favourite club): if you put your hand under a green light, no light will go through it, whilst doing the same under a red light the result will be very different. That means that red light is less absorbed by our body. Near infrared light is even less absorbed and this is why this region of the spectrum is ideal for in vivo imaging. Therefore, we made our cells to absorb strongly in the near infrared so we can easily distinguish them.

Gold nanoparticles of different sizes and shapes (synthesis and picture by Joan Comenge).

Gold nanoparticles of different sizes and shapes (synthesis and picture by Joan Comenge).

To do this, we labelled cells with gold nanoparticles. Interestingly, the way gold nanoparticles interact with light depends on how their electrons oscillate. That means that size and shape of the nanoparticles determine their optical properties, and this is one of the reasons why we love to make different shapes of nanoparticles. In particular, gold nanorods strongly absorb in the near infrared and they are ideal contrast agents for in vivo imaging.


Figure reproduced from: The production of sound by radiant energy; Science 28 May 1881; DOI: 10.1126/science.os-2.49.242

We have now cells that interact with light in a different way than the tissue. The problem is that light is scattered by tissue, so resolution is rapidly lost as soon as you try to image depths beyond 1 mm. Obviously, this is not the best for in vivo imaging. Luckily for us, Alexander Graham Bell realised 130 years ago that matter emits sounds when is irradiated by a pulsed light. This is known as the photoacoustic effect and it has been exploited recently for bioimaging. Photoacoustic imaging combines the advantages of optical imaging (sensitivity, real-time acquisition, molecular imaging) and the good resolution of ultrasound imaging because ultrasounds (or phonons), contrarily to photons, are not scattered by biological tissue.
GNR-35.2Si3 in cells_16

Silica-coated gold nanorods inside cells

To optimise the performance of our gold nanorods, we coated them with silica. Silica is glass and therefore it protects the gold core without interfering with its optical properties. This protection is required to maintain gold nanorods isolated inside cells since nanorods are entrapped in intracellular vesicles, where they are very packed. The absence of a protective coating ultimately would result in a broader and less intense absorbance band, which would be translated to a less intense photoacoustic signal and consequently a lower sensitivity in cell detection. This of special importance in our system, a photoacoustic imaging system developed by iThera Medical which uses a  multiwavelength excitation to later deconvolute the spectral information of the image to find your components of interest. Thus, narrow absorption bands helps to improve the detection sensitivity even further. With this we demonstrated that we were able to monitor a few thousand nanorods labelled-cells with a very good 3D spatial resolution for 15 days. This allowed for example to see how a cell cluster changed with time, see how it grows or which regions of the cell cluster shows the highest cell density. In addition, this work opens the door to new opportunities such as  multilabelling using gold nanorods of different sizes and consequently different optical properties to observe simultaneously different type of cells. We also believe that not only stem cell therapies, but also other fields that are interested in monitoring cells such as cancer biology or immunology can benefit from the advances described in our work.

You can find the original publication here (or here*).
All the datasets are available via Figshare.

This work was supported by the UK Regenerative Medicine Platform Safety and efficacy, focusing on imaging technologies. Joan Comenge was funded by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme. The in vivo imaging was done in the Centre for Preclinical Imaging, the Electron Microscopy in the Biomedical EM unit and the Optical Microscopy in the Centre for Cell Imaging.

* the alternative link is to 50 free e-prints; the link will be removed once the paper is fully open access (in a couple of days).


Cluster of gold nanorod-labelled cells imaged by photoacoustic imaging three days after implantation in mice.

Nano talk for 15 years old

About two weeks ago, the Institute received an inquiry from Shevington High School near Wigan (~ 30 min drive from Liverpool). Clare Ingham, a student teacher in the School, wrote:

Recently I’ve been discussing nanoscience and nanotechnology with my year 10 students. They were very interested and enthused on the work that is being led in the north west in this area. 

Indeed, you can see on the School news blog that they really enjoyed making some model fullerenes some weeks ago [scroll down on that page to “Year 10 Chemistry”]. Clare continued:

I’d like to keep that enthusiasm high by hopefully inviting one of your research team to the school to give a short talk/Q&A with a small number of pupils in the near future on some Liverpool led developments in nanotechnology? Would this be a possibility? I’m keen to enthuse the pupils of the science they could be part of and leading in the future.

I volunteered. I have done some outreach talks before, e.g. Christmas lecture and Scibar, but I thought I’d ask Twitter for new ideas. Thank you to @Zen_of_Science@bardmital@drheaddamage@DaveFernig@PSBROOKES and @medickinson for their suggestions which I have collected in this Spotify (send me more ideas via twitter and I’ll add them there).

I visited this morning.

I was introduced as a “distinguished scientist”. I asked the children if I looked like a “distinguished scientist”. One was brave enough to say “no”. I told them a little bit my study and career path. Then, I presented to them some real “distinguished scientist” via this picture of three members of my group at a conference in France. The aim was to challenge their (?) preconceptions about scientists and make it clear that scientists look very much like them. That was not so much inspired by the Twitter response but more by my former student Rachel Gilbert’s project, the excellentThis is what a scientist looks likeas well as what I learnt through my involvement in the Institute Athena Swan committee.

We moved to “nanotechnology”. I asked them what “nano” meant. They replied:

Very small. So small you can’t see

That was a good start but of course everything is relative; 1 meter is very small compared to the Earth-Sun distance. We need to be more precise. How small is very small? From meter to millimeter, from millimeter to micrometer and finally from micrometer to nanometer. Next, I asked them for things which have dimensions in this range. Their responses, after a bit of prompting, included:

red blood cells, viruses, fullerenes and atoms

A really good base for discussion. Red blood cells a bit big for nano? Atoms, a bit small? Viruses and fullerenes: spot on! I added a few biological ingredients: proteins, DNA, membranes. I then remarked that there were two types of objects in our list. One student did get the hint and said “Biological versus non-biological” which led me to introduce how we can make things on the nanoscale via either top-down (carving a block of matter) or bottom-up (assembling parts, or better, self-assembly although I did not really get into that). Nanotechnology is in their everyday life. It is even in their pockets. I showed them this picture of how a state-of-the-art computer looked like when my parents were born. It filled a room and was infinitely less powerful than their mobile phone. I also showed them pictures of a modern transistor and of the kind of gigantic plants which are required to make these.

I asked them what they knew about light.

travel in a straight line.

speed of light is 300 ooo km/s.

white light can be separated into different colors.

I pushed a bit more on the differences between colors and a student mentioned “wavelength” but they could not really explain what this was nor how small/big were the wavelengths of visible light. Visible light is nano (blue ~ 400 nm, green ~ 520 nm, red ~ 600 nm). Nano is everywhere 😉

Since we are scientists, we do experiments. I asked for two volunteers. Before I could say one more word, I had plenty of hands up. I then specified that I required a sample from those volunteers (at that points, I think there was a hint of worry in the teacher’s eyes) but I quickly explained that I required only one hair from each (the worry dissipated). We did the hair experiment with the laser pointer as suggested by @drheaddamage (check his videos here and here). Before doing the experiment, we tried to predict the result. Given their everyday experience of light and the fact that they learnt that light travel in a straight line, the prediction is what we should see a shadow of the hair in the laser spot. The reality is quite different. We see a scattering line perpendicular to the hair with maxima and minima along the line. This is due to the fact that light is a wave. I used this experiment to show one way by which we can get information on the size of things we can’t see.

Gold nanoparticles in water

Gold nanoparticles in water. Looks like Ribena.


We then moved to nanoparticles, first gold, and then superparamagnetic iron oxide nanoparticles.

The superparamagnetic nanoparticles are also quite fascinating as you can move the liquid around with a magnet and even defy gravity (picture below).

To conclude my presentation and link with our current research efforts, I explained the need to track STEM cells in the body and how those nanoparticles, both the superparamagnetic iron oxide nanoparticles and the gold nanorods, can be developed as contrast agents for animal/human imaging.


Superparamagnetic nanoparticles in solvent. The liquid is held up by the magnet.


Update: Proof that I have been there; from Shevington High School news:

Today: Imaging Workshop and Prelaunch of the University of Liverpool’s new Centre for Preclinical Imaging

Imaging Workshop and Prelaunch of the University of Liverpool’s new Centre for Preclinical Imaging

4th September 2013, Sherrington Lecture Theatre 1 (311 on campus map)


During the next academic session, the University of Liverpool will be opening a Centre for Preclinical Imaging. The Centre, which will be based in the Physiology building within the Institute of Translational Medicine, aspires to provide all of the key imaging modalities currently used for small animal whole-body imaging. Apart from providing state-of-the-art imaging facilities for researchers working with small animals, a key aim of the Centre will be to collaborate with physical scientists, including chemists, physicists, engineers, mathematicians and computer scientists, in order to develop multi-modal imaging strategies, next generation imaging technologies and novel imaging probes.


11:00-11:15   Chris Sanderson (Head of the Department of Physiology, University of Liverpool)

         “Introducing the University of Liverpool’s Centre for Preclinical Imaging”

11:15-12:00   Harald Groen* (MILabs)

        “Preclinical in-vivo imaging modalities and their applications”

12:00-12:45   Pai-Chi Li* (Institute of Biomedical Electronics & Bioinformatics, National Taiwan University)

“Applications of ultrasound in small animal imaging”

12:45-13:30   Lunch

13:30-14:00   Philippe Choquet* (Dept of Nuclear Physics, Hopitaux Universitaires de Strasbourg)

 “Pre-clinical field MR in small animal imaging and its inputs to multi-modality work”

14:00-14:45  Michael Gyngell* (MRI applications manager, Agilent Technologies)

“Applications of high-field magnetic resonance (MR) in small animal imaging”

14:45-15:30   Freek Beekman* (Delft University of Technology and CEO of MILabs)

“Applications of computed tomography (CT) and the nuclear imaging technologies, single positron  emission computed tomography (SPECT) and positron emission tomography (PET) in small animal  imaging”

15:30-15:50   Coffee break

15:50-16:20    Francois Lassailly* CRUK

Applications of fluorescence and bioluminescence in small animal imaging”

16:20-16:50   Raphael Lévy (Institute of Integrative Biology, University of Liverpool)

 “Photothermal and photoacoustic imaging for cell and small animal imaging”

16:50-1715     Trish Murray (Institute of Translational Medicine, University of Liverpool)

“An overview of the Centre for Preclinical Imaging: current status; predicted timescales for    completion and installation of imaging platforms; information on how it will operate.”


*Biographies of external speakers

Dr Harald Groen Dr. Harald Groen is an application scientist at MILabs,  supporting  scientists using MILabs’ SPECT,  PET and multi-modal imaging devices.  He studied BioMedical Engineering and obtained his PhD at the Erasmus MC, Rotterdam, the Netherlands on shear stress and atherosclerosis. After his PhD he was a post-doctoral researcher at the department of Nuclear Medicine, studying neuroendocrine tumors with SPECT and PET in animal models. In addition, he was coordinator of the Applied Molecular Imaging Facility of the Erasmus MC, a platform for scientists who share state-of-the-art imaging technology – like ultrasound, micro-CT, MRI, optical, SPECT and PET imaging – and molecular assays for studying biological systems.  As such, he has a broad experience in multi-modal preclinical imaging.  h.groen@milabs.com

Professor Pai-Chi Li is IEEE Fellow, IAMBE Fellow and AIUM Fellow. He is also Editor-in-Chief of Journal of Medical and Biological Engineering, Associate Editor of Ultrasound in Medicine and Biology, Associate Editor of IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, and on the Editorial Board of Ultrasonic Imaging and Photoacoustics. He has received numerous awards, including the 2012 Distinguished Research Award from National Science Council, the 2011 National Innovation Award, the 2011 Distinguished Innovation Research Reward from National Taiwan University, the 2009 Distinguished Research Award from National Science Council. He was also recipient of the Distinguished Achievement Award in Electrical Engineering: Systems in 1994 for his outstanding academic achievement at the University of Michigan. paichi@cc.ee.ntu.edu.tw

Dr Michael Gyngell is an employee of Agilent Technologies and has the role of European MRI Applications Lab Manager at Agilent’s facility in Oxford. He has a distinguished career in MRI, contributing to the field both as an engineer & scientist, in industry as well as in academia, for over 30 years. He is author or co-author of more than 50 journal articles and many conference proceedings. He has also served on the board of trustees of the ISMRM (International Society of Magnetic Resonance in Medicine). michael.gyngell@agilent.com

Dr Philippe  Choquet is a Senior Lecturer in Biophysics and Nuclear Medicine, and since 2011, has been head of the Preclinical Imaging Lab, department of the Strasbourg University Hospitals. He is the author and coauthor of more than 50 papers in peer-reviewed journals as well as more than 100 oral and poster communications in national and international meetings in the field of low field MRI, MR elastography, NMR/MRI of hyperpolarized gases, tomographic reconstruction, small animal scintigraphy and µCT.pchoquet@unistra.fr

Professor Freek Beekman is head of the section Radiation, Detection & Medical Imaging at Delft University of Technology. He has (co-)authored more than 100 peer reviewed journal papers, several book chapters and over 20 patent applications and was presented with several national & international awards for his scientific contributions to biomedical imaging. His research interest includes development of detectors, image reconstruction for SPECT, PET, X-ray CT & hybrid imaging devices. Freek is an editorial board member of the International Journal of Biomedical Imaging and Physics in Medicine & Biology. He is also the founder and CEO of Molecular Imaging Laboratories (www.milabs.com) that markets systems with an unsurpassed spatial and temporal resolution. Recently, MILabs received the Frost & Sullivan Product Innovation Award for VECTor, the first system that performs SPECT and PET imaging simultaneously at sub-mm resolution level. f.beekman@milabs.com

Dr Francois Lassailly is head of the In Vivo Imaging Facility at the London Research Institute – Cancer Research UK, which he started to develop in 2007. After an initial training in Immunology and Cellular Engineering Francois worked for 7 years in different academic and private Cell Therapy laboratories. He then had the opportunity to develop Patient Derived Xenograft models of human leukaemia and to manage the Tumour Biobank of the Paoli Calmettes Institute (regional cancer centre of Marseille, France). He did his PhD at the London Research Institute (LRI – CRUK), working on multimodal and multiscale optical imaging of haematopoietic stem cell niches in the bone marrow during which he initiated the core in vivo imaging activity by implanting 3 imaging modalities. In 2010 he received his PhD and was directly hired by the institute to lead and develop the In Vivo Imaging Facility which is now offering whole body optical imaging (fluorescence and bioluminescence), intravital microscopy, x-ray microCT and high resolution ultrasound. He is now becoming involved with the development of the in vivo imaging facility for the new Francis Crick Institute, which is to open in 2015. Francois.Lassailly@cancer.org.uk

First symposium on nanoparticle-based technologies for cell tracking: concluding remarks

The symposium was at the same time highly focused and highly diverse.

The focus came from the theme, i.e nanomaterials for cell tracking which is still a relatively new scientific field (the first few reviews on this topic have been published in the past 2 years, including our own). The diversity came from the combination of expertise and approaches required to achieve that aim: MRI with magnetic particles (and other labels), gold nanoparticles for photoacoustic imaging, of quantum dots for fluorescence imaging, but also of dye-loaded silica particles and silicon quantum dots. The diversity also came from the biological problems addressed that included (non-exhaustive) a better understanding of immuno cell therapy in cancer, understanding of metastasis and several models of tissue regeneration with stem cells. As a result of this diversity, I have learnt a lot and my impression is that most attendees had the same experience (but if not, please protest in the comment box!).

As one of the organizers, two of my duties were to organize the poster prize award and to chair the round table discussion that ended the meeting. For the former, we opted for a democratic protocol: instead of a jury of senior scientists choosing the winner, we gave every attendees a vote. The idea was to encourage everyone to engage as much as possible in the poster session. It worked well: 31 participants voted. The winner, Sofia Pereira, had a poster evaluating the feasibility of using genetically encoded markers (such as ferritin) for labelling. A lot of her results were extremely interesting but most would fit in the category of #negativeresults, i.e. things are much more difficult than what has been published in the literature. It is encouraging that such results were valued and I hope she will be able to publish well this work.

For the round table, nothing had been decided before the beginning of the meeting except for the fact that I was going to chair it. My aim was to (at a small scale) ‘restore the role of discussion in academic meetings’. The settings were not ideal: a lecture theatre and no round table, but, nevertheless, we did manage to create the atmosphere and get the discussion going. We spent a good hour discussing what are the current challenges in the field. Most attendees present, from PhD students to Professors contributed to the discussion – some insightful comments also from a Bruker representative (about Magnetic Particle Imaging) and from Felicity Sartain (nanoKTN). The final result from the round table discussion is shown below…

cell tracking round table

Thank you to all speakers, poster presenters and attendees. Thank you to Jane Remmer (PA to Matt Rosseinsky) and Arthur Taylor (PDRA in Patricia Murray’s group) who did a tremendous work in organizing the symposium. Thank you also to our sponsors listed below.

Should we do it again?

What can we Learn by Watching Cells Moving Towards a Magnet?

Andor has just published a technical note from Lara Bogart. That follows from their visit of our lab a couple of weeks ago.

Lara Bogart from Raphael Levy’s research group at the Institute of Integrative Biology in University of Liverpool is interested in understanding how magnetic nanoparticles interact with cells; this is important for a range of biomedical applications including diagnosis of disease, hyperthermia therapy and stem cell tracking applications.

Read on.