This page contains the operating procedures for the AOMC equipment. Follow these procedures while working with the equipment to ensure optimal performance and durability. If you have any questions regarding these procedures or want to request a specific procedure, please contact AOMC staff.

Additionally, you can find a selection of interesting microscopy resources (articles, tutorials, tools, ...), and a list of publications in collaboration with AOMC.

GFP Large Png GFP Large Png

Operating procedures, guides and manuals

Zeiss LSM880 NLO Airyscan

Basic instructions: Download the SOP here.

  • switching the system ON
  • switching the system OFF
  • cleaning procedures

Confocal experimental setup: Download the SOP here.

  • mounting a sample
  • locating a sample
  • multi-color experiment
  • z-stack experiment (3D)
  • time series experiment (movies, timelapse)
  • tilescan experiment (larger sample areas)
  • data storage principles

Airyscan experimental setup: Download the SOP here.

  • Airyscan setup
  • Airyscan FAST setup

Zeiss LSM510 meta

Coming soon.

Zeiss Elyra PS.1

Basic instructions: Download the SOP here.

  • switching the system ON
  • switching the system OFF
  • cleaning procedures

Nikon Eclipse Ti2-E

Basic instructions: Download the SOP here.

  • switching the system ON
  • switching the system OFF
  • cleaning procedures


Thorlabs S175C powermeter (high power):

Setting up the S175C high intensity powermeter sensor to measure the power of the pulsed lasers (e.g. MaiTai).

Download the S175C powermeter instructions here.

Thorlabs S170C powermeter (low power):

Setting up the S170C low intensity powermeter sensor to measure the output power of the continuous lasers (e.g. Argon or HeNe).

Download the S170C powermeter instructions here.

Interesting resources

A selection of interesting microscopy articles and reviews:

  • Jonkman, J., Brown, C. M., Wright, G. D., Anderson, K. I. & North, A. J. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc (2020) doi:10.1038/s41596-020-0313-9.
  • Jimenez, A., Friedl, K. & Leterrier, C. About samples, giving examples: Optimized Single Molecule Localization Microscopy. Methods 174, 100–114 (2020). doi:10.1016/j.ymeth.2019.05.008.
  • North, A. J. Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. J Cell Biol 172, 9–18 (2006). doi:10.1083/jcb.200507103.

A selection of interesting microscopy resources:

A selection of interesting video resources and tutorials:

A selection of interesting fluorophore and filter resources:



CD36-mediated uptake of myelin debris by macrophages and microglia reduces neuroinflammation.

Grajchen E, Wouters E, van de Haterd B, et al.
J Neuroinflammation. 2020;17(1):224. doi:10.1186/s12974-020-01899-x

Zeiss LSM880
multicolor - confocal

Monitoring indoor exposure to combustion-derived particles using plants.

Witters K, Plusquin M, Slenders E, et al.
Environmental Pollution. 2020;266:115261. doi:10.1016/j.envpol.2020.115261

Zeiss LSM880 and Zeiss LSM510
NLO - 2PE - spectral detection - label-free

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis.

Van den Broek B, Pintelon I, Hamad I, et al.
J Extracell Vesicles. 2020;10(1). doi:10.1002/jev2.12022

Zeiss LSM880
multicolor - confocal

Nano-positioning and tubuline conformation determine transport of mitochondria along microtubules.

Van Steenbergen V, Lavoie-Cardinal F, Kazwiny Y, et al.
bioRxiv. 2020. doi:10.1101/2020.04.27.064766

Zeiss Elyra PS.1
live-cell - TIRF

Stearoyl-CoA desaturase-1 impairs the reparative properties of macrophages and microglia in the brain.

Bogie JFJ, Grajchen E, Wouters E, et al.
J Exp Med. 2020;217(5). doi:10.1084/jem.20191660

Zeiss LSM880
3D - multicolor - confocal

Fluorescence microscopy data for quantitative mobility and interaction analysis of proteins in living cells.

Lemmens V, Ramanathan K, Hendrix J.
Data in Brief. 2020;29:105348. doi:10.1016/j.dib.2020.105348

Zeiss LSM880
live-cell - RICS - spectral detection - confocal

Angiogenic Effects of Human Dental Pulp and Bone Marrow-Derived Mesenchymal Stromal Cells and their Extracellular Vesicles.

Merckx G, Hosseinkhani B, Kuypers S, et al.
Cells. 2020;9(2):312. doi:10.3390/cells9020312

Zeiss LSM880
multicolor - confocal

(Sub)populations of extracellular vesicles released by TNF-α –triggered human endothelial cells promote vascular inflammation and monocyte migration.

Hosseinkhani B, van den Akker NMS, Molin DGM, Michiels L.
Journal of Extracellular Vesicles. 2020;9(1):1801153. doi:10.1080/20013078.2020.1801153

Zeiss LSM880

Live Cell Imaging Demonstrates Multiple Routes Toward a STAT1 Gain-of-Function Phenotype.

Giovannozzi S, Lemmens V, Hendrix J, Gijsbers R, Schrijvers R.
Front Immunol. 2020;11. doi:10.3389/fimmu.2020.01114

Zeiss LSM880
live-cell - RICS - confocal

Dental Tissue and Stem Cells Revisited: New Insights From the Expression of Fibroblast Activation Protein-Alpha.

Driesen RB, Hilkens P, Smisdom N, et al.
Front Cell Dev Biol. 2020;7. doi:10.3389/fcell.2019.00389

Zeiss LSM880
NLO - 2PE - SHG - label-free - confocal - multicolor

Raster Image Correlation Spectroscopy Performance Evaluation.

Longfils M, Smisdom N, Ameloot M, et al.
Biophysical Journal. 2019;117(10):1900-1914. doi:10.1016/j.bpj.2019.09.045

Zeiss LSM880
live-cell - RICS - confocal

Ambient black carbon particles reach the fetal side of human placenta.

Bové H, Bongaerts E, Slenders E, et al.
Nature Communications. 2019;10(1):3866. doi:10.1038/s41467-019-11654-3

Zeiss LSM880 and Zeiss LSM510
NLO - 2PE - SHG - spectral detection - label-free

Role of nanoparticle size and sialic acids in the distinct time-evolution profiles of nanoparticle uptake in hematopoietic progenitor cells and monocytes.

Wathiong B, Deville S, Jacobs A, et al.
Journal of Nanobiotechnology. 2019;17(1):62. doi:10.1186/s12951-019-0495-x

Zeiss LSM880
3D - multicolor - Airyscan - 2PE

Effect of Branching on the Optical Properties of Poly(p-phenylene ethynylene) Conjugated Polymer Nanoparticles for Bioimaging.

Braeken Y, Cheruku S, Seneca S, et al.
ACS Biomater Sci Eng. 2019;5(4):1967-1977. doi:10.1021/acsbiomaterials.8b01416

Zeiss LSM880
live-cell - 2PE - NLO

Body surface area-based versus concentration-based intraperitoneal perioperative chemotherapy in a rat model of colorectal peritoneal surface malignancy: pharmacologic guidance towards standardization.

Lemoine L, Thijssen E, Carleer R, et al.
Oncotarget. 2019;10(14):1407-1424. doi:10.18632/oncotarget.26667

Zeiss Elyra PS.1
multicolor - widefield - SIM

Fluorescent PCDTBT Nanoparticles with Tunable Size for Versatile Bioimaging. Materials.

Cheruku S, D’Olieslaeger L, Smisdom N, et al.
Materials. 2019;12(15):2497. doi:10.3390/ma12152497

Zeiss LSM880 and Zeiss LSM510
live-cell - RICS - 2PE - NLO - confocal

SlZRT2 Encodes a ZIP Family Zn Transporter With Dual Localization in the Ectomycorrhizal Fungus Suillus luteus.

Coninx L, Smisdom N, Kohler A, et al.
Front Microbiol. 2019;10. doi:10.3389/fmicb.2019.02251

Zeiss LSM880 and Zeiss Elyra PS.1
live-cell - confocal - widefield - multicolor

Image Correlation Spectroscopy with Second Harmonic Generating Nanoparticles in Suspension and in Cells.

Slenders E, Bové H, Urbain M, et al.
J Phys Chem Lett. 2018;9(20):6112-6118. doi:10.1021/acs.jpclett.8b02686

Zeiss LSM880 and Zeiss LSM510
ICS - NLO - SHG - 2PE - labelfree

Crosstalk-free multicolor RICS using spectral weighting.

Schrimpf W, Lemmens V, Smisdom N, Ameloot M, Lamb DC, Hendrix J.
Methods. 2018;140-141:97-111. doi:10.1016/j.ymeth.2018.01.022

Zeiss LSM880
live-cell - RICS - spectral detection - confocal


Sam Duwé - AOMC

Agoralaan, Building C, 3590 Diepenbeek
Microscopy expert