Ihor Smal: Image Analysis, Smart Microscopy and AI

CV – Research – Lab members – Publications

 

Dr. Ihor Smal
Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University
Kruytgebouw, room Z509
Padualaan 8, 3584 CH Utrecht
The Netherlands
Email: i.v.smal@uu.nl

 

Curriculum Vitae

Ihor Smal studied physics and electrical engineering at Ivan Franko National University of Lviv, Ukraine (M.Sc. degree (cum laude) 1999), where he later worked as a research scientist (1999-2002), carrying out research in the field of nonlinear dynamical systems and chaos. From 2003 to 2005, he was a research assistant (postmaster program “Mathematics for Industry”) at the department of Mathematics and Computer Science of Eindhoven University of Technology, the Netherlands. In 2005 he graduated on the project “Design and implementation of a six camera scanning unit” and was awarded a Professional Doctorate in Engineering degree (PDEng). From 2005 to 2009 he was a PhD student at Biomedical Imaging Group Rotterdam (BIGR, Erasmus University/MC), the Netherlands, conducting research on motion registration and analysis in cellular and molecular bioimaging, defending the thesis entitled “Particle Filtering Methods for Subcellular Motion Analysis” (2009).

From February 2009 to 2018 he was a postdoctoral fellow at the Departments of Medical Informatics and Radiology of the Erasmus MC in Rotterdam, the Netherlands, conducting research on several topics defined by the personal grants (VENI, Erasmus MC Fellowship and NWO BBoL grant). From 2019 to 2020 he was an assistant professor at the department of Geoscience and Remote Sensing, TU Delft working on statistical and machine learning methods for optical and laser remote sensing. In 2020 he returned to the field of bioimaging as an assistant professor at the Erasmus MC, Biomedical Sciences Theme, working in collaboration with several research groups at the departments of Cell Biology and Molecular Genetics, developing methods for motion analysis and image understanding using modern statistical and AI methods. Since 2023, he is an assistant professor at Utrecht University, division of Cell Biology, Neurobiology and Biophysics, heading the lab on statistical image analysis, smart microscopy and explainable AI methods.

 

Research summary

Our research focuses on combining statistical signal and image processing with advanced data modeling, with a particular focus on motion analysis in biological systems. The goal is to bridge the gap that exists between developing pure methodological advances in computer vision and machine learning and solving challenging real-world applications with high societal impact, which can benefit from using modern AI techniques. We strive to move from pure image processing and analysis to completely automated image/data understanding, based on machine learning and artificial intelligence. This will provide exciting new opportunities for the study and understanding of living systems.

We are part of the NWO IMAGINE! (“Innovative Microscopy and Guidance of cells In their Native Environment”) programme (Tech. Work Package 2) aiming at the development of high-precision control strategies that will enable automated real-time manipulation of key aspects of the biological systems. Our main focus is on development of novel solutions for real-time image processing and image analysis using explainable AI approaches that will be used for automated real-time optimization of imaging experiments, to control cellular architecture, migration and fate with light and provide feedback to the imaging systems to achieve automated guidance of biological processes.

You can find more information about our current activities and possible research projects on our webpage: www.smal.ws

 

Lab members

PhD students:  
Vincent Hellebrekers v.j.w.hellebrekers@uu.nl
Daan te Rietmole d.m.a.terietmole@uu.nl

 

Publications

For the most up-to-date list of publication click here

2024

Zwijnen AW, Watzema L, Ridwan Y, van Der Pluijm I, Smal I, Essers J. Self-adaptive deep learning-based segmentation for universal and functional clinical and preclinical CT image analysis. Comput Biol Med. 2024 Sep;179:108853. doi: 10.1016/j.compbiomed.2024.108853. Epub 2024 Jul 15. PMID: 39013341.

Y Yao, I Smal, I Grigoriev, A Akhmanova, E Meijering , Deep Joint Denoising and Detection for Enhanced Intracellular Particle Analysis arXiv preprint arXiv:2408.07903.

Paul MW, Aaron J, Wait E, Van Genderen RM, Tyagi A, Kabbech H, Smal I, Chew TL, Kanaar R, Wyman C. Distinct mobility patterns of BRCA2 molecules at DNA damage sites. Nucleic Acids Res. 2024 Aug 12;52(14):8332-8343. doi: 10.1093/nar/gkae559. PMID: 38953170.

H Kabbech, I Smal , TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning, Journal of Open Source Software 9 (98), 6157.

TH de Wolf, D Roman, J Nonnekens, I Smal , Weakly Supervised 3d Image Segmentation in Fluorescence Microscopy Using Maximum Intensity Projections, 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 1-4.

VJW Hellebrekers, JB Passmore, LC Kapitein, I Smal, An Iterative Frequency-Based Approach for Gelmap Grid Deformation Correction, 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 1-4.

Lieke Stockmann, Hélène Kabbech, Gert-Jan Kremers, Brent van Herk, Bas Dille, Mirjam van den Hout, Wilfred F.J. van IJcken, Dick Dekkers, Jeroen A.A. Demmers, Ihor Smal, Danny Huylebroeck, Sreya Basu, Niels Galjart, KIF2A maintains cytokinesis in mouse embryonic stem cells by stabilising intercellular bridge microtubules, bioRxiv 2024.07.11.603034; doi: https://doi.org/10.1101/2024.07.11.603034.

Hellebrekers VJW, van Walsum T, Smal I, Cornelissen SAP, van Zwam WH, van der Lugt A, van der Sluijs M, Su R. Automated image registration of cerebral digital subtraction angiography. Int J Comput Assist Radiol Surg. 2024 Jan;19(1):147-150. doi: 10.1007/s11548-023-02999-8. Epub 2023 Jul 17. PMID: 37458928.

2023

Yavuz S, Kabbech H, van Staalduinen J, Linder S, van Cappellen WA, Nigg AL, Abraham TE, Slotman JA, Quevedo M, Poot RA, Zwart W, van Royen ME, Grosveld FG, Smal I, Houtsmuller AB. Compartmentalization of androgen receptors at endogenous genes in living cells. Nucleic Acids Res. 2023 Nov 10;51(20):10992-11009. doi: 10.1093/nar/gkad803. PMID: 37791849; PMCID: PMC10639085.

H Kabbech, J van Staalduinen, F Grosveld, I Smal , Accurate Estimation of Particle Dynamics Bypassing Substrate Drift Bias: Application to Cell Nucleus Motion 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 1-4.

TH de Wolf, M Snelders, J Essers, I Smal, CA-LIME: An Algorithm that Explains Classification Results of Cardiomyocyte Beating, 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 1-4.

2022

Meijering, I. Smal, O. Dzyubachyk, J. C. Olivo-Marin, Motion Tracking and Analysis, Microscope Image Processing (2nd Edition), Academic Press, September 2022, Ch. 14, pp. 393–430.

Zwijnen AW, Watzema L, Ridwan Y, van Der Pluijm I, Smal I, Essers J. Self-adaptive deep learning-based segmentation for universal and functional clinical and preclinical CT image analysis. Comput Biol Med. 2024 Sep;179:108853. doi: 10.1016/j.compbiomed.2024.108853. Epub 2024 Jul 15. PMID: 39013341.

Klaus A, Clapes T, Yvernogeau L, Basu S, Weijts B, Maas J, Smal I, Galjart N, Robin C. CLASP2 safeguards hematopoietic stem cell properties during mouse and fish development. Cell Rep. 2022 Jun 14;39(11):110957. doi: 10.1016/j.celrep.2022.110957. PMID: 35705037.

H Kabbech, I Smal , Identification of diffusive states in tracking applications using unsupervised deep learning methods, 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI), 1-4.

2021

Muñoz-Gil G, Volpe G, Garcia-March MA, Aghion E, Argun A, Hong CB, Bland T, Bo S, Conejero JA, Firbas N, Garibo I Orts Ò, Gentili A, Huang Z, Jeon JH, Kabbech H, Kim Y, Kowalek P, Krapf D, Loch-Olszewska H, Lomholt MA, Masson JB, Meyer PG, Park S, Requena B, Smal I, Song T, Szwabiński J, Thapa S, Verdier H, Volpe G, Widera A, Lewenstein M, Metzler R, Manzo C. Objective comparison of methods to decode anomalous diffusion. Nat Commun. 2021 Oct 29;12(1):6253. doi: 10.1038/s41467-021-26320-w. PMID: 34716305.

Lin Z, Wu B, Paul MW, Li KW, Yao Y, Smal I, Proietti Onori M, Hasanbegovic H, Bezstarosti K, Demmers J, Houtsmuller AB, Meijering E, Hoebeek FE, Schonewille M, Smit AB, Gao Z, De Zeeuw CI. Protein Phosphatase 2B Dual Function Facilitates Synaptic Integrity and Motor Learning. J Neurosci. 2021 Jun 30;41(26):5579-5594. doi: 10.1523/JNEUROSCI.1741-20.2021. Epub 2021 May 21. PMID: 34021041.

Lo CSY, van Toorn M, Gaggioli V, Paes Dias M, Zhu Y, Manolika EM, Zhao W, van der Does M, Mukherjee C, G S C Souto Gonçalves J, van Royen ME, French PJ, Demmers J, Smal I, Lans H, Wheeler D, Jonkers J, Chaudhuri AR, Marteijn JA, Taneja N. SMARCAD1-mediated active replication fork stability maintains genome integrity. Sci Adv. 2021 May 5;7(19):eabe7804. doi: 10.1126/sciadv.abe7804. PMID: 33952518.

W Zhao, EM Manolika, AR Chaudhuri, I Smal, Detection Of Replication Forks In Em Images Using Faster R-Cnn, 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 1786-1789.

2020

Serra-Marques A, Martin M, Katrukha EA, Grigoriev I, Peeters CA, Liu Q, Hooikaas PJ, Yao Y, Solianova V, Smal I, Pedersen LB, Meijering E, Kapitein LC, Akhmanova A. Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends. Elife. 2020 Nov 11;9:e61302. doi: 10.7554/eLife.61302. PMID: 33174839; PMCID: PMC7710357.

Yao Y, Smal I, Grigoriev I, Akhmanova A, Meijering E. Deep-learning method for data association in particle tracking. Bioinformatics. 2020 Dec 8;36(19):4935-4941. doi: 10.1093/bioinformatics/btaa597. PMID: 32879934.

Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E. Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Development. 2020 May 26;147(10):dev184861. doi: 10.1242/dev.184861. PMID: 32253238.

Ma H, Smal I, Daemen J, Walsum TV. Dynamic coronary roadmapping via catheter tip tracking in X-ray fluoroscopy with deep learning based Bayesian filtering. Med Image Anal. 2020 Apr;61:101634. doi: 10.1016/j.media.2020.101634. Epub 2020 Jan 11. PMID: 31978856.

Serra-Marques A, Martin M, Katrukha EA, Grigoriev I, Peeters CA, Liu Q, Hooikaas PJ, Yao Y, Solianova V, Smal I, Pedersen LB, Meijering E, Kapitein LC, Akhmanova A. Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends. Elife. 2020 Nov 11;9:e61302. doi: 10.7554/eLife.61302. PMID: 33174839; PMCID: PMC7710357.

2019

Arts M, Smal I, Paul MW, Wyman C, Meijering E. Particle Mobility Analysis Using Deep Learning and the Moment Scaling Spectrum. Sci Rep. 2019 Nov 20;9(1):17160. doi: 10.1038/s41598-019-53663-8. PMID: 31748591; PMCID: PMC6868130.

Zhou, K., Chen, Y., Smal, I., and Lindenbergh, R.: BUILDING SEGMENTATION FROM AIRBORNE VHR IMAGES USING MASK R-CNN, Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLII-2/W13, 155–161, https://doi.org/10.5194/isprs-archives-XLII-2-W13-155-2019, 201.

Mata G, Radojević M, Fernandez-Lozano C, Smal I, Werij N, Morales M, Meijering E, Rubio J. Automated Neuron Detection in High-Content Fluorescence Microscopy Images Using Machine Learning. Neuroinformatics. 2019 Apr;17(2):253-269. doi: 10.1007/s12021-018-9399-4. PMID: 30215167.

I Smal, Y Yao, N Galjart, E Meijering, Facilitating data association in particle tracking using autoencoding and score matching, 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019).

2018

Y Yao, I Smal, E Meijering, Deep neural networks for data association in particle tracking, 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).

I Smal, N Galjart, E Meijering, Accurate estimation of intracellular dynamics and underlying spatial structures using hierarchical trajectory smoothing 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018).

2017

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C. An objective comparison of cell-tracking algorithms. Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30. PMID: 2908340.

Yang C, Wu J, de Heus C, Grigoriev I, Liv N, Yao Y, Smal I, Meijering E, Klumperman J, Qi RZ, Akhmanova A. EB1 and EB3 regulate microtubule minus end organization and Golgi morphology. J Cell Biol. 2017 Oct 2;216(10):3179-3198. doi: 10.1083/jcb.201701024. Epub 2017 Aug 16. PMID: 28814570; PMCID: PMC5626540.

I Smal, S Basu, L Sayas, N Galjart, E Meijering, Gaussian processes for trajectory analysis in microtubule tracking applications, 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017).

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C. An objective comparison of cell-tracking algorithms. Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30. PMID: 29083403.

Yao Y, Smal I, Grigoriev I, Martin M, Akhmanova A, Meijering E. Automated Analysis of Intracellular Dynamic Processes. Methods Mol Biol. 2017;1563:209-228. doi: 10.1007/978-1-4939-6810-7_14. PMID: 28324611.

Sun W, Poot DHJ, Smal I, Yang X, Niessen WJ, Klein S. Stochastic optimization with randomized smoothing for image registration. Med Image Anal. 2017 Jan;35:146-158. doi: 10.1016/j.media.2016.07.003. Epub 2016 Jul 6. PMID: 27423112.

Ambrosini P, Smal I, Ruijters D, Niessen WJ, Moelker A, Van Walsum T. A Hidden Markov Model for 3D Catheter Tip Tracking With 2D X-ray Catheterization Sequence and 3D Rotational Angiography. IEEE Trans Med Imaging. 2017 Mar;36(3):757-768. doi: 10.1109/TMI.2016.2625811. Epub 2016 Nov 7. PMID: 27845655.

2016

Yu N, Signorile L, Basu S, Ottema S, Lebbink JHG, Leslie K, Smal I, Dekkers D, Demmers J, Galjart N. Isolation of Functional Tubulin Dimers and of Tubulin-Associated Proteins from Mammalian Cells. Curr Biol. 2016 Jul 11;26(13):1728-1736. doi: 10.1016/j.cub.2016.04.069. Epub 2016 Jun 9. PMID: 27291054.

Radojević M, Smal I, Meijering E. Fuzzy-Logic Based Detection and Characterization of Junctions and Terminations in Fluorescence Microscopy Images of Neurons. Neuroinformatics. 2016 Apr;14(2):201-19. doi: 10.1007/s12021-015-9287-0. PMID: 26701809; PMCID: PMC4823367.

2015

Isabel Schlangen, José Franco, Jérémie Houssineau, William TE Pitkeathly, Daniel Clark, Ihor Smal, Colin Rickman, Marker-less stage drift correction in super-resolution microscopy using the single-cluster PHD filter, 2015 IEEE Journal of Selected Topics in Signal Processing 10 (1), 193-202.

Smal I, Meijering E. Quantitative comparison of multiframe data association techniques for particle tracking in time-lapse fluorescence microscopy. Med Image Anal. 2015 Aug;24(1):163-189. doi: 10.1016/j.media.2015.06.006. Epub 2015 Jun 27. PMID: 26176413.

M Radojevié, I Smal, E Meijering, Automated neuron morphology reconstruction using fuzzy-logic detection and Bayesian tracing algorithms 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), 885-888.

Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C. BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells. J Cell Biol. 2014 Dec 8;207(5):599-613. doi: 10.1083/jcb.201405014. Erratum in: J Cell Biol. 2015 Mar 16;208(6):857. doi: 10.1083/jcb.20140501402182015c. PMID: 25488918; PMCID: PMC4259808.

Basu S, Sladecek S, Martinez de la Peña y Valenzuela I, Akaaboune M, Smal I, Martin K, Galjart N, Brenner HR. CLASP2-dependent microtubule capture at the neuromuscular junction membrane requires LL5β and actin for focal delivery of acetylcholine receptor vesicles. Mol Biol Cell. 2015 Mar 1;26(5):938-51. doi: 10.1091/mbc.E14-06-1158. Epub 2015 Jan 14. PMID: 25589673.