MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description



Nanosciences and Nanotechnologies, third-level study programme


prof. dr. Cornelis Johannes Forrendinis Van Noorden


The aim of the course is to give students practical and theoretical insight and overview of the imaging techniques and methodologies that are available these days to image cells, tissues and organs in the most true-to-nature conditions possible. The insights and overview creates a basis for the students to select the right imaging techniques in their further career in applied or fundamental research.


The course Bioimaging deals with the revolutionary new developments in bioimaging from the level of non-invasive imaging in live animals, 4D imaging of live cells and tissues (organoids) down to microscopy and nanoscopy. The Nobel prizes for the developments of fluorescent proteins in cell biology in 2008 and for nanoscopy in 2014 demonstrate the importance of the techniques. They have given cell and tissue biology completely new dimensions. In the course, the various approaches in bioimaging will be learned:
- Non-invasive imaging in live animals
- Imaging of cells, organoids and tissues in vitro
- Confocal microscopy
- Fluorescence versus absorbance
- In situ hybridization, immunohistochemistry
and metabolic mapping by enzyme histochemistry
- Transmission and scanning electron microscopy
- Combined light and electron microscopy (CLEM1)
- 4D (time and space) imaging of live cells with controlled light exposure microscopy (CLEM2)
- Nanoscopy (superresolution) with STED and PALM
- Image cytometry and image analysis
- Flow cytometry and cell sorting

Course literature:

1. Alberts B et al (2015) Chapter 9: Visualizing Cells in Molecular Biology of the Cell (6th edn) Garland Science, New York, pp 529-564.

2. Van Noorden CJF (2010) Imaging enzymes at work: metabolic mapping by enzyme histochemistry. J Histochem Cytochem 58:481-497.

3. Chieco P et al (2013) Image cytometry: protocols for 2D and 3D quantification in microscopic images. Progr Histochem Cytochem 47:211-233

4. Eggeling C et al (2015) Lens-based fluorscence nanoscopy. Quart Rev Biophys

Significant publications and references:

The acquired theoretical ad practical knowledge will be acquired during selective lectures and consultations. It is also possible to include the students into experimental research in the laboratory.

CJF Van Noorden, 2014. Metabolic Mapping by (Quantitative) Enzyme Histochemstry. Pathobiology of Humon Diseases: A dynamic Encyclopedia of Disease Mechanisms, pp 3760-3774

V Krishnaswami, CJF Van Noorden, EMM Manders & RA Hoebe, 2014. Towards digital photon counting cameras for single-molecule optical nanoscopy. Opt Nanoscopy 3:1

J Ramos de Carvalho, FD Verbraak, MC Aalders, CJF Van Noorden & RO Schlingerman, 2014. Recent advances in ophthalmic molecular imaging. Surv Ophthalmol 59, 393-413

RA Hoebe, CJF Van Noorden & EMM Manders, 2010. Noise effects and filtering in controlled light exposure microscopy. J Microsc 240, 197-206

IMC Vogels, KA Hoeben & CJF Van Noorden, 2008. Rapid combined light and electron microscopy on large frozen biological samples. J Microsc 235, 252-258

PC De Witt Hamer, S Leenstra, CJF Van Noorden & AH Zwinderman, 2009. Organotypic glioma spheroids for screening of experimental therapies: how many spheroids and sections are required. Cytometry Part A 75A, 528-534

RA Hoebe, HTM Van der Voort, J Stap. CJF Van Noorden & EMM Manders, 2008. Quantitative determination of the reduction of phototoxicity and photobleaching by controlled light exposure microscopy. J Microsc 231, 9-20

ORF Mook, A Jonker, AC Strang, A Veltien, G Gambarota, WM Frederiks, A Heerschap & CJF Van Noorden, 2008. Noninvasive magnetic resonance imaging of the development of individual colon cancer tumors in rat liver. BioTechniques 44, 529-535

CPW Klerk, RM Overmeer, TMH Niers, HH Versteeg, DJ Richel, T Buckle, CJF Van Noorden & Olaf Tellingen, 2007. Validity of bioluminescence measurements for noninvasive in vivo imaging of tumor load in small animals. BioTechniques 43, S7-S13

RA Hoebe, CH Van Oven, TWJ Gadella, PB Dhonuskshe, CJF Van Noorden & EMM Manders, 2007. Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging. Nat Biotechnol 25, 249-255


Oral presentation (70%)
Writing essay (30%)

Students obligations:

Oral presentation.
Writing essay.