Dr Chas Nelson

  • Lord Kelvin/Adam Smith Research Fellow in Data Science (School of Physics & Astronomy)

Research interests

Personal webpage: http://www.chasnelson.co.uk

Research Interests

My research interests focus on two scientific areas:

  1. Understanding how the retina learns to processing visual stimuli.
  2. The interface of hardware, software and wetware in the pursuit of high quality, quantitative bioimaging.

Both of these areas requires the integration of skills from computing, engineering, chemistry and the life sciences. As such, my research career has moved me between disciplines and involves a large number of cross-disciplinary collaborations.

You can find my publications here.

Current Research

How can babies see from the moment their born? How does the retina learn to process images before sending them to the brain? My current research is aimed at understanding these fundamental neuroscience questions by combining state-of-the-art light sheet microscopy, image analysis and network science.

I am doing this in the zebrafish (Danio Rerio), a popular model organism in microscopy due to it’s optical transparency and the wide range of fluorescence transgenic lines now available. Zebrafish are even more attractive as models for retinal developmental biology due to their relative simplicity but core similarities to mammalian retinal development.

researcherID: F-5524-2015


Publications

List by: Type | Date

Jump to: 2019 | 2018 | 2017 | 2015 | 2014
Number of items: 11.

2019

Alharbi, S. S., Sazak, Ç., Nelson, C. J. , Alhasson, H. F. and Obara, B. (2019) The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images. Methods, (doi:10.1016/j.ymeth.2019.05.025) (PMID:31176770) (In Press)

Sazak, Ç., Nelson, C. J. and Obara, B. (2019) The multiscale bowler-hat transform for blood vessel enhancement in retinal images. Pattern Recognition, 88, pp. 739-750. (doi:10.1016/j.patcog.2018.10.011)

Nelson, C. J. , Jackson, P. T.G. and Obara, B. (2019) Combining mathematical morphology and the Hilbert transform for fully automatic nuclei detection in fluorescence microscopy. In: Burgeth, B., Kleefeld, A., Naegel, B., Passat, N. and Perret, B. (eds.) Mathematical Morphology and Its Applications to Signal and Image Processing: 14th International Symposium, ISMM 2019, SaarbrĂĽcken, Germany, July 8-10, 2019, Proceedings. Series: Lecture notes in computer science (11564). Springer: Cham, pp. 532-543. ISBN 9783030208660 (doi:10.1007/978-3-030-20867-7_41)

2018

Alharbi, S. S., Sazak, Ç., Nelson, C. J. and Obara, B. (2018) Curvilinear Structure Enhancement by Multiscale Top-Hat Tensor in 2D/3D Images. In: IEEE International Conference on Bioinformatics and Biomedicine, Madrid, Spain, 3-6 Dec 2018, (In Press)

Sazak, Ç., Nelson, C. J. and Obara, B. (2018) The Multiscale Bowler-Hat Transform for Vessel Enhancement in 3D Biomedical Images. In: British Machine Vision Conference 2018, Newcastle upon Tyne, UK, 3-6 Sep 2018,

Nelson, C. , Buckley, C., Mullins, J. J., Denvir, M. A. and Taylor, J. (2018) Imaging the Developing Heart: Synchronized Timelapse Microscopy During Developmental Changes. In: SPIE BiOS, San Francisco, CA., 27-28 Jan 2018, (doi:10.1117/12.2290191)

2017

Willcocks, C. G., Jackson, P. T.G., Nelson, C. , Nasrulloh, A. V. and Obara, B. (2017) Interactive GPU active contours for segmenting inhomogeneous objects. Journal of Real-Time Image Processing, (doi:10.1007/s11554-017-0740-1) (Early Online Publication)

Willcocks, C. G., Jackson, P. T.G., Nelson, C. and Obara, B. (2017) Extracting 3D parametric curves from 2D images of Helical objects. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(9), pp. 1757-1769. (doi:10.1109/TPAMI.2016.2613866) (PMID:28114058)

2015

Jackson, P. T.G., Nelson, C. , Schiefele, J. and Obara, B. (2015) Runway Detection in High Resolution Remote Sensing Data. In: 2015 9th International Symposium on Image and Signal Processing and Analysis (ISPA), Zagreb, Croatia, 07-09 Sep 2015, pp. 170-175. ISBN 9781467380324 (doi:10.1109/ISPA.2015.7306053)

2014

Nelson, C. , Duckney, P., Hawkins, T. J., Deeks, M. J., Laissue, P. P., Hussey, P. J. and Boguslaw, O. (2014) Blobs and curves: object-based colocalisation for plant cells. Functional Plant Biology, 42(5), pp. 471-485. (doi:10.1071/FP14047)

Nelson, C. J. , Dixon, M., Laissue, P. P. and Obara, B. (2014) Speeding Up Active Mesh Segmentation by Local Termination of Nodes. In: Medical Image Understanding and Analysis (MIUA 2014), Egham, UK, 09-11 Jul 2014, pp. 179-184. ISBN 9781901725513

This list was generated on Tue Nov 12 20:17:15 2019 GMT.
Number of items: 11.

Articles

Alharbi, S. S., Sazak, Ç., Nelson, C. J. , Alhasson, H. F. and Obara, B. (2019) The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images. Methods, (doi:10.1016/j.ymeth.2019.05.025) (PMID:31176770) (In Press)

Sazak, Ç., Nelson, C. J. and Obara, B. (2019) The multiscale bowler-hat transform for blood vessel enhancement in retinal images. Pattern Recognition, 88, pp. 739-750. (doi:10.1016/j.patcog.2018.10.011)

Willcocks, C. G., Jackson, P. T.G., Nelson, C. , Nasrulloh, A. V. and Obara, B. (2017) Interactive GPU active contours for segmenting inhomogeneous objects. Journal of Real-Time Image Processing, (doi:10.1007/s11554-017-0740-1) (Early Online Publication)

Willcocks, C. G., Jackson, P. T.G., Nelson, C. and Obara, B. (2017) Extracting 3D parametric curves from 2D images of Helical objects. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(9), pp. 1757-1769. (doi:10.1109/TPAMI.2016.2613866) (PMID:28114058)

Nelson, C. , Duckney, P., Hawkins, T. J., Deeks, M. J., Laissue, P. P., Hussey, P. J. and Boguslaw, O. (2014) Blobs and curves: object-based colocalisation for plant cells. Functional Plant Biology, 42(5), pp. 471-485. (doi:10.1071/FP14047)

Book Sections

Nelson, C. J. , Jackson, P. T.G. and Obara, B. (2019) Combining mathematical morphology and the Hilbert transform for fully automatic nuclei detection in fluorescence microscopy. In: Burgeth, B., Kleefeld, A., Naegel, B., Passat, N. and Perret, B. (eds.) Mathematical Morphology and Its Applications to Signal and Image Processing: 14th International Symposium, ISMM 2019, SaarbrĂĽcken, Germany, July 8-10, 2019, Proceedings. Series: Lecture notes in computer science (11564). Springer: Cham, pp. 532-543. ISBN 9783030208660 (doi:10.1007/978-3-030-20867-7_41)

Conference Proceedings

Alharbi, S. S., Sazak, Ç., Nelson, C. J. and Obara, B. (2018) Curvilinear Structure Enhancement by Multiscale Top-Hat Tensor in 2D/3D Images. In: IEEE International Conference on Bioinformatics and Biomedicine, Madrid, Spain, 3-6 Dec 2018, (In Press)

Sazak, Ç., Nelson, C. J. and Obara, B. (2018) The Multiscale Bowler-Hat Transform for Vessel Enhancement in 3D Biomedical Images. In: British Machine Vision Conference 2018, Newcastle upon Tyne, UK, 3-6 Sep 2018,

Nelson, C. , Buckley, C., Mullins, J. J., Denvir, M. A. and Taylor, J. (2018) Imaging the Developing Heart: Synchronized Timelapse Microscopy During Developmental Changes. In: SPIE BiOS, San Francisco, CA., 27-28 Jan 2018, (doi:10.1117/12.2290191)

Jackson, P. T.G., Nelson, C. , Schiefele, J. and Obara, B. (2015) Runway Detection in High Resolution Remote Sensing Data. In: 2015 9th International Symposium on Image and Signal Processing and Analysis (ISPA), Zagreb, Croatia, 07-09 Sep 2015, pp. 170-175. ISBN 9781467380324 (doi:10.1109/ISPA.2015.7306053)

Nelson, C. J. , Dixon, M., Laissue, P. P. and Obara, B. (2014) Speeding Up Active Mesh Segmentation by Local Termination of Nodes. In: Medical Image Understanding and Analysis (MIUA 2014), Egham, UK, 09-11 Jul 2014, pp. 179-184. ISBN 9781901725513

This list was generated on Tue Nov 12 20:17:15 2019 GMT.

Research datasets

Jump to: 2019
Number of items: 1.

2019

Taylor, J., Nelson, C. , Bruton, F. A., Baghbadrani, A. K., Buckley, C., Tucker, C. S., Mullins, J. J. and Denvir, M. A. (2019) Hybrid optical gating for long-term 3D time-lapse imaging of the beating embryonic zebrafish heart. [Data Collection]

This list was generated on Tue Nov 12 14:42:26 2019 GMT.