Recent preprints

3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets

Kugler E. C., Frost J, Silva V., Plant K., Chhabria K., Chico T. J.A. and Armitage P. A.

bioRxiv 2020.08.06.239905; doi:

The effect of absent blood flow on the zebrafish cerebral and trunk vasculature

Elisabeth Kugler, Ryan Snodgrass, George Bowley, Karen Plant, Jovana Serbanovic-Canic, Paul C. Evans, Timothy Chico, Paul Armitage

bioRxiv 2020.07.23.216192; doi:

Segmentation of the Zebrafish Brain Vasculature from Light Sheet Fluorescence Microscopy Datasets

Kugler E. C., Rampun A.., Chico T. J.A. and Armitage P. A.

bioRxiv 2020.07.21.213843; doi:


* Corresponding Author



Conference Paper, Kugler E.*, Chico T. and Armitage P., Validating Segmentation of the Zebrafish Vasculature, In: Zheng Y., Williams B., Chen K. (eds) Medical Image Understanding and Analysis. MIUA 2019. Communications in Computer and Information Science, vol 1065. Springer, Cham (Link)

Journal Article, Kugler E.*, van Lessen M., Daetwyler S., Chhabria K., Savage A., Silva V., Plant K., McDonald R., Huisken J., Wilkinson R., Schulte-Merker S., Armitage P. and Chico T.*, Cerebrovascular Endothelial Cells form Transient Notch-Dependent Cystic Structures in Zebrafish, EMBO Reports (Link)

Conference Abstract, Kugler E., Chhabria K., Daetwyler S., Plant K., Savage A., Wilkinson R., Armitage P., Chico T.J.A., Endothelial Cells Form Transient Cystic Structures During Zebrafish Cerebrovascular Development, Cardiovasc Drugs Ther (2019) 33: 261. (Link)

Journal Article, Kugler E.*, Plant K., Chico T. and Armitage P., Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature, Journal of Imaging, MDPI, Vol. 5, Issue 1. (Link)

Journal Article, Chhabria K., Plant K., Bandmann O., Wilkinson R., Martin C., Kugler E., Armitage P., Santoscoy P., Cunliffe V., Howarth C.*, and Chico T.*, The Effect of Hyperglycemia on Neurovascular Coupling and Cerebrovascular Patterning in Zebrafish., JCBF (Link)

Conference Paper, Kugler E.*, Chico T. and Paul A., Image Analysis in Light Sheet Fluorescence Microscopy Images of Transgenic Zebrafish Vascular Development, In: Nixon, M., Mahmoodi, S. and Zwiggelaar, R., (eds.) Medical Image Understanding and Analysis. MIUA 2018, 09-11 Jul 2018, Southampton, UK. Communications in Computer and Information Science, 894 . Springer Nature Switzerland AG , pp. 343-353. ISBN 9783319959207 (Link)


Journal Article, Rieder D.*, Amort T., Kugler E., Lusser A. and Trajanoski Z., meRanTK: Methylated RNA Analysis ToolKit, Bioinformatics. 2016 Mar 1;32(5):782-5. doi: 10.1093/bioinformatics/btv647. Epub 2015 Nov 4. (Link)


Conference Paper, Schwerte T.*, Stolz S. and Kugler E., Preparing and Publishing Wikipedia Articles are a good Tool to train Project Management, Teamwork and Peer Reviewed publishing Processes in Life Sciences, In: Improving University Teaching. Proceedings of the 37th International Conference "Fostering Knowledge Transfer - Improving University Teaching" (Link)