Dr John Halpin

Marine image analyst and modeller

I am a marine image analyst leading in this field at SAMS, with over four years’ experience in biological image analysis. I have previously worked at Cancer Research UK’s Beatson Institute developing custom image analysis pipelines, including deep learning methods with CNNs.  I am currently leading the image analysis component of three projects, involving the latest techniques, such as custom deep learning pipelines for the automatic recognition of flora and fauna and photogrammetry/3D modelling.

Prior to working as an image analyst, I completed two Postdocs in advanced Transmission Electron Microscopy, which included developing new energy materials, and a PhD in semiconductor physics.

Contact details:

I am interested in answering biological questions through the optimised acquisition and processing of underwater images.


Current projects

North Sea 3D: Measuring and predicting marine growth on man-made structures by converting industry and bespoke ROV survey footage into 3D models with automatic faunal identification. Funded by NERC INSITE; 2021-24

SEA-AI: Streamlined and efficient artificial-intelligence assisted underwater video analysis. 2022-24

First author peer-reviewed publications

Halpin JE, Jenkins B, Moody MP, Webster RWH, Bos J-WG, Bagot PAJ, and MacLaren DA (2022) A Correlative Study of Interfacial Segregation in a Cu-Doped TiNiSn Thermoelectric half-Heusler Alloy. ACS Applied Electronic Materials https://doi.org/10.1021/acsaelm.2c00699 

Halpin JE, Webster RHW, Gardner H, Moody MP, Bagot PAJ, MacLaren DA (2019) An in-situ approach for preparing atom probe tomography specimens by xenon plasma-focussed ion beam. Ultramicroscopy 202: 121-127 https://doi.org/10.1016/j.ultramic.2019.04.005 

Halpin JE, Rhead SD, Sanchez AM, Myronov M, Leadley DR (2015) Growth of complex SiGe/Ge superlattices by reduced pressure chemical vapour deposition at low temperature. Semiconductor Science and Technology 30(11): 114009 https://doi.org/10.1088/0268-1242/30/11/114009 


Co-authored publications

Henry He, John E Halpin, Srinivas R Popuri, Luke Daly, Jan-Willem G Bos, Michael P Moody, Donald A MacLaren, Paul AJ Bagot (2021) Atom Probe Tomography of a Cu-Doped TiNiSn Thermoelectric Material: Nanoscale Structure and Optimization of Analysis Conditions. Microscopy and Microanalysis 28(4): 1340-1347 https://doi.org/10.1017/S1431927621012162 

David Boldrin, Eduardo Mendive-Tapia, Jan Zemen, Julie B Staunton, Angelo M Gomes, Luis Ghivelder, John Halpin, Alexandra S Gibbs, Araceli Aznar, Josep-Lluís Tamarit, Pol Lloveras, Xavier Moya, Lesley F Cohen (2021) Baricaloric properties of quaternary Mn3(Zn,In)N for room-temperature refrigeration applications. Physical Review B 104(13): 134101 https://doi.org/10.1103/PhysRevB.104.134101 

Luke Daly, MR Lee, P Bagot, John Halpin, W Smith, S McFadzean, AC O’Brien, S Griffin, LJ Hallis, BE Cohen (2020) Exploring Mars at the nanoscale: Applications of transmission electron microscopy and atom probe tomography in planetary exploration. IOP Conference Series: Materials Science and Engineering 891(1): 012008 https://doi.org/10.1088/1757-899X/891/1/012008 

SM Lambrick, L Vozdecký, M Bergin, JE Halpin, DA MacLaren, PC Dastoor, SA Przyborski, AP Jardine, DJ Ward (2020) Multiple scattering in scanning helium microscopy. Applied Physics Letters 116(6) 061601 https://doi.org/10.1063/1.5143950 

RWH Webster, JE Halpin, Srinivasa R Popuri, J-WG Bos, DA MacLaren (2019) Spontaneous formation of nanostructures during pulsed laser deposition of epitaxial half-Heusler TiNiSn on MgO. APL Materials 7(1): 013206 https://doi.org/10.1063/1.5052361 

SA Barczak, RJ Quinn, JE Halpin, K Domosud, RI Smith, AR Baker, E Don, I Forbes, K Refson, DA MacLaren, JWG Bos (2019) Suppression of thermal conductivity without impeding electron mobility in n-type XNiSn half-Heusler thermoelectrics. Journal of Materials Chemistry A 7(47): 27124-27134 https://doi.org/10.1039/C9TA10128D 

Daniella A Ferluccio, John E Halpin, Kathryn L MacIntosh, Robert J Quinn, Eric Don, Ronald I Smith, Donald A MacLaren, Jan-Willem G Bos (2019) Low thermal conductivity and promising thermoelectric performance in A x CoSb (A=V, Nb or Ta) half-Heuslers with inherent vacancies. Journal of Materials Chemistry C 7(22): 6539-6547 https://doi.org/10.1039/C9TC00743A 

Sonia A Barczak, John E Halpin, Jim Buckman, Rodolphe Decourt, Michael Pollet, Ronald I Smith, Donald A MacLaren, Jan-Willem G Bos (2018) Grain-by-grain compositional variations and interstitial metals - A new route toward achieving high performance in half-Heusler thermoelectrics. ACS Applied Materials & Interfaces 10(5): 4786-4793 https://doi.org/10.1021/acsami.7b14525 

M Myronov, C Morrison, J Halpin, S Rhead, J Foronda, D Leadley (2015) Revealing high room and low temperature mobiligies of 2D holes in a strained Ge quantum well heterostructures grown on a standard Si substrate. Solid-State Electronics 110: 35-39  https://doi.org/10.1016/j.sse.2015.01.012 

VA Shah, SD Rhead, J Finch, M Myronov, JS Reparaz, RJ Morris, NR Wilson, V Kachkanov, IP Dolbnya, JE Halpin, D Patchett, P Allred, G Colston, KJS Sawhney, CM Sotomayor Torres, DR Leadley (2015) Electrical properties and strain distribution of Ge suspended structures. Solid-State Electronics 108: 13-18 https://doi.org/10.1016/j.sse.2014.12.004 

J Foronda, C Morrison, JE Halpin, SD Rhead, M Myronov (2014) Weak antilocalization of high mobility holes in a strained Germanium quantum well heterostructure. Journal of Physics: Condensed Matter 27(2): 022201 https://doi.org/10.1088/0953-8984/27/2/022201 

VA Shah, M Myronov, SD Rhead, JE Halpin, Andrey Shchepetov, MJ Prest, Mika Prunnila, TE Whall, EHC Parker, DR Leadley (2014) Flat single crystal Ge membranes for sensors and opto-electronic integrated circuitry. Solid-State Electronics 98: 93-98 https://doi.org/10.1016/j.sse.2014.04.015 

Rhead SD, Halpin JE, Shah VA, Myronov M, Patchett DH, Allred PS, Kachkanov V, Dolbnya IP, Reparaz JS, Wilson NR, Sotomayor Torres CM, Leadley DR (2014) Tensile strain mapping in flat Gemanium membranes. Applied Physics Letters 104(17): 172107 https://doi.org/10.1063/1.4874836 

VA Shah, SD Rhead, JE Halpin, O Trushkevych, E Chávez-Ángel, Andrey Shchepetov, V Kachkanov, NR Wilson, M Myronov, JS Reparaz, RS Edwards, MR Wagner, F Alzina, IP Dolbnya, DH Patchett, PS Allred, MJ Prest, PM Gammon, M Prunnila, TE Whall, EHC Parker, CM Sotomayor Torres, DR Leadley (2014) High quality single crystal Ge nano-membranes for opto-electronic integrated circuitry. Journal of Applied Physics 115(14): 144307 https://doi.org/10.1063/1.4870807 

Trushkevych O, Shah VA, Myronov M, Halpin JE, Rhead SD, Prest MJ, Leadley DR, Edwards RS (2014) Laser-vibrometric ultrasonic characterization of resonant modes and quality factors of Ge membranes. Science and Technology of Advanced Materials 15(2): 025004 https://doi.org/10.1088/1468-6996/15/2/025004 

Myronov M, Morrison C, Halpin J, Rhead S, Casteleiro C, Foronda J, Shah VA, Leadley D (2014) An extreme high room temperature mobility of two-dimensional holes in a stained Ge quantum well heterostructure grown by reduced pressure chemical vapor deposition. Japanese Journal of Applied Physics 53(4S): 04EH02 https://doi.org/10.7567/JJAP.53.04EH02 

Trushkevych O, Shah VA, Myronov M, Halpin JE, Rhead SD, Prest MJ, Leadley DR, Edwards RS (2014) Laser-based ultrasonic characterisation of Ge membranes. Sci Techol Adv 

Ulyanenkova T, Benediktovitch A, Myronov M, Halpin J, Rhead S, Ulyanenkov A (2014) Stress of homogeneous and graded epitaxial thin films studied by full-shape analysis of high resolution reciprocal space maps. Materials Science Forum 768: 249-256 https://doi.org/10.4028/www.scientific.net/MSF.768-769.249 

Mironov OA, Hassan AHA, Uhlarz M, Kiatgamolchai S, Dobbie A, Morris RJH, Halpin JE, Rhead SD, Allred P, Myronov M, Gabani S, Berkutov IB, Leadley DR (2013) New RP-CVD grown ultra-high performance selectively B-doped pure-Ge 20nm QWs on Si as basis material for post-Si CMOS technology. Physica Status Solidi 11(1) 61-64 https://doi.org/10.1002/pssc.201300164 

Ulyanenkova T, Myronov M, Benediktovitch A, Mikhalychev A, Halpin J, Ulyanenkov A (2013) Characterization of SiGe thin films using a laboratory X-ray instrument. Journal of Applied Crystallography 46(4): 898-902 https://doi.org/10.1107/S0021889813010492 

Kelsall RW, Dinh VT, Ivanov P, Valavanis A, Lever LJM, Ikonic Z, Velha P, Dumas D, Gallacher KF, Paul DJ, Halpin J, Myrnov M, Leadley DR (2013) Germanium/silicon heterostructures for terahertz emission. ECS Transactions 50(9): 763 https://doi.org/10.1149/05009.0763ecst 


Employment history

2 years Biological Image Analyst. Cancer Research UK

5 years Postdoctoral Researcher. University of Glasgow



2015 PhD Semiconductor Physics. University of Warwich

2011 MRes Semiconductor Physics