IMPORTANT: Histology services at Covid-19 Re-Entry operation

For detailed information on the current facility operations, please click here.

Histology – the power to reveal unexpected connections

Histology, the science of studying microscopic structure of the cells, tissues, and organs, provides crucial information to understand the relationship between structure and function of biological machinery.

The Histology Facility offers versatile equipment and expert knowledge that allow researchers to preserve and visualize microanatomy of their model organisms.

Our services encompass tissue processing, routine histological stains, a growing array of immunostaining techniques and in situ hybridization methods. We are dedicated to develop highly individualized approaches for each project.

Do you work with tissue systems or animal models? Do you study disease processes? Are you interested in our services?  


Experimental design and protocol planning

We can assist with study design, and development and implementation of protocols for standard as well as customized experimental studies.

Preanalytical procedures

We routinely provide services and support for:

  • Sample collection, fixation, and processing
  • Cryo- and paraffin embedding and sectioning
  • Staining

We have experience working with several types of samples including whole organisms, isolated organs, slices or groups of tissues, cell cultures (2D and 3D), fluids, and inorganic materials.

We perform routine and special histochemical stains along with immunostainings (immunofluorescence, immunohistochemistry, and multiplex stains). We have experience with background reduction in problematic “mouse on mouse” stainings as well as cross-reactivity avoidance during multiplex stainings. We also offer RNA in situ hybridization with basic protocols and RNAscope.

Auxiliary services

Support during self-service is offered exclusively to IMP/IMBA/GMI members. It includes training in the use of all the sectioning equipment available in the facility and troubleshooting support.

Secondary and inter-facility support includes coordinated processing services (e.g., perfusion and dissection after in vivo imaging) offered with other facilities for multimodal projects. For example, HistoPathology staff work collaboratively with the IMP Biooptics core facility to facilitate whole slide digitization (slide scanning).


A fully open immunostaining system with the capacity for 60 slides per run. It can perform immunochemistry staining with either DAB or AP-red detection systems using customized protocols.

If you are interested in having immunostains done on your samples with the i6000, please contact us.

This instrument performs automatic tissue dehydration, clearing, and paraffin infiltration of up to 360 tissue cassettes in one run.

If you are interested in using the Donatello, please contact us.

Microtome to section frozen or cryo-embedded tissues. Open-top cryostat with ergonomic design for working while standing or sitting. This cryostat allows a section thickness range from 0.5 to 100 µm. The temperature for the specimen clumper is controlled and ranges from 10°C to -35°C. There is a separate temperature control for the knife carrier down to -35°C.

Heavy duty microtomes used for paraffin sectioning, allowing a section thickness range from 0.5 to 100 µm. The sections can then be transferred onto a glass slide and used for a wide variety of staining protocols (basic staining, immunohistochemistry, in situ hybridization, or immunofluorescence).

Please click here for more equipment.


To order a service, please contact the facility staff as early as possible to discuss relevant details and agree upon timelines. When submitting samples, please remember to label each sample with a unique identifier (e.g., mouse ID or organoid batch number), submitter initials, and date. Please also provide relevant details such as: genotype, treatment, or other procedure.I f procedures relevant to coordinated processing have been performed (e.g. in vivo imaging), please ensure that pertinent details and representative images are provided. The clearer and more complete the information provided, the lower the risk of downstream errors. The facility can also provide you with submission forms for your projects.

IMP, IMBA, and GMI researchers can, by themselves, use all sectioning equipment in the facility, but only after attending a training session with our staff. To set up an appointment for training, please contact the facility staff.  

In addition, the facility offers many for-fee-services to members of the Vienna BioCenter (academic institutions and companies) as well as external academic institutions and private companies.

For paid service projects, the users from the Vienna BioCenter have priority. Otherwise, the service projects are performed in the order they are requested; ‘first come, first served’.

We require acknowledgement of facility use in publications. 
A simple statement is sufficient and can be placed in the Materials and Methods section or in the Acknowledgments section, depending on the journal format.

Suggested format:

The XXXXXX was performed by the Histopathology Facility 
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

In case of (co-)authorship:

The Vienna BioCenter Core Facilities (VBCF) Histopathology Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna.


Fennell LM, Gomez Diaz C, Deszcz L, Kavirayani A, Hoffmann D, Yanagitani K, Schleiffer A, Mechtler K, Hagelkruys A, Penninger J, Ikeda F. [2020] Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling. EMBO J. 39(24):e103303

Apelin inhibition prevents resistance and metastasis associated with anti‐angiogenic therapy

Uribesalgo I, Hoffmann D, Zhang Y, Kavirayani A, Lazovic J, Berta J, Novatchkova M, Pai TP, Wimmer RA, László V, Schramek D, Karim R, Tortola L, Deswal S, Haas L, Zuber J, Szűcs M, Kuba M., Dome B, Cao Y, Haubner BJ, Penninger JM. EMBO Mol Med. 2019 Aug; 11(8)

HACE1 deficiency leads to structural and functional neurodevelopmental defects

Nagy V, Hollstein R, Pai TP, Herde MK, Buphamalai P, Moeseneder P, Lenartowicz E, Kavirayani A, Korenke GC, Kozieradzki I, Nitsch R, Cicvaric A, Monje Quiroga FJ, Deardorff MA, Bedoukian EC, Li Y, Yigit G, Menche J, Perçin EF, Wollnik B, Henneberger C, Kaiser FJ, Penninger JM, Neurol Genet Jun 2019, 5 (3) e330

Cdk6 coordinates Jak2V617F mutant MPN via NFκB and apoptotic networks

Uras IZ, Maurer B, Nivarthi H, Jodl P, Kollmann K, Prchal-Murphy M, Milosevic Feenstra JD, Zojer M, Lagger S, Grausenburger R, Grabner B, Holly R, Kavirayani A, Bock C, Gisslinger H, Valent P, Kralovics R, Sexl V, Blood. 2019 Apr; 133(15)

Precocious expression of Blimp1 in B cells causes autoimmune disease with increased self-reactive plasma cells

Bönelt P, Wöhner M, Minnich M, Tagoh H, Fischer M, Jaritz M, Kavirayani A, Garimella M, Karlsson MCI, Busslinger M. EMBO J. 2019 Jan; 38(2).

Genetically engineered cerebral organoids model brain tumor formation.

Bian S, Repic M, Guo Z, Kavirayani A, Burkard T, Bagley JA, Krauditsch C & Knoblich JA, Nat. Methods. 2018 Aug; 15(8): 631-639.


Natural killer cell-intrinsic type I IFN signaling controls Klebsiella pneumoniae growth during lung infection

Ivin M, Dumigan A, de Vasconcelos FN, Ebner F, Borroni M, Kavirayani A, Przybyszewska KN, Ingram RJ, Lienenklaus S, Kalinke U, Stoiber D, Bengoechea JA, Kovarik P, PLoS Pathog. 2017 Nov; 13(11): e1006696.

Linear ubiquitination by LUBEL has a role in Drosophila heat stress response.

Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F, EMBO Rep. 2016 Nov; 17(11): 1624-1640.

Inhibition of CBLB protects from lethal Candida albicans sepsis.

Wirnsberger G, Zwolanek F, Asaoka T, Kozieradzki I, Tortola L, Wimmer RA, Kavirayani A, Fresser F, Baier G, Langdon WY, Ikeda F, Kuchler K, Penninger JM, Nat Med. 2016 Aug; 22(8): 915-923

RANKL/RANK control Brca1 mutation-driven mammary tumors.

Sigl V, Owusu-Boaitey K, Joshi PA, Kavirayani A, Wirnsberger G, Novatchkova M, Kozieradzki I, Schramek D, Edokobi N, Hersl J, Sampson A, Odai-Afotey A, Lazaro C, Gonzalez-Suarez E, Pujana MA, Cimba F, Heyn H, Vidal E, Cruickshank J, Berman H, Sarao R, Ticevic M, Uribesalgo I, Tortola L, Rao S, Tan Y, Pfeiler G, Lee EY, Bago-Horvath Z, Kenner L, Popper H, Singer C, Khokha R, Jones LP, Penninger JM, Cell Res. 2016 Jul; 26(7): 761-774.


A high sensitivity ZENK monoclonal antibody to map neuronal activity in Aves. Nordmann, G.C., Malkemper, E.P., Landler, L. et al. [2020] Sci Rep 10, 915

The amygdala instructs insular feedback for affective learning. Kargl D, Kaczanowska J, Ulonska S, Groessl F, Piszczek L, Lazovic J, Buehler K, Haubensak W. [2020] Elife. 9:e60336.

A human tissue screen identifies a regulator of ER secretion as a brain-size determinant. Esk C, Lindenhofer D, Haendeler S, Wester RA, Pflug F, Schroeder B, Bagley JA, Elling U, Zuber J, von Haeseler A, Knoblich JA. [2020] Science. 370(6519):935-941.

A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans. Hagelkruys A, Wirnsberger G, Stadlmann J, Wöhner M, Horrer M, Vilagos B, Jonsson G, Kogler M, Tortola L, Novatchkova M, Bönelt P, Hoffmann D, Koglgruber R, Steffen U, Schett G, Busslinger M, Bergthaler A, Klein C, Penninger JM. [2020] J Exp Med. 218(1):e20200559.

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Borg M, Jacob Y, Susaki D, LeBlanc C, Buendía D, Axelsson E, Kawashima T, Voigt P, Boavida L, Becker J, Higashiyama T, Martienssen R, Berger F. [2020] Nat Cell Biol. 22(6):621-629

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. [2020] Curr Biol. 30(4):573-588.e7.

Loss of histone macroH2A1 in hepatocellular carcinoma cells promotes paracrine-mediated chemoresistance and CD4+CD25+FoxP3+ regulatory T cells activation. Lo Re O, Mazza T, Giallongo S, Sanna P, Rappa F, Vinh Luong T, Li Volti G, Drovakova A, Roskams T, Van Haele M, Tsochatzis E, Vinciguerra M. [2020] Theranostics 10(2):910-924.

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection. Colaço HG, Barros A, Neves-Costa A, Seixas E, Pedroso D, Velho T, Willmann KL, Faisca P, Grabmann G, Yi HS, Shong M, Benes V, Weis S, Köcher T, Moita LF. [2020] Immunity. 54(1):53-67.e7

3D Printing of large-scale and highly porous biodegradable tissue engineering scaffolds from poly(trimethylene-carbonate) using two-photon-polymerization. Weisgrab G, Guillaume O, Guo Z, Heimel P, Slezak P, Poot A, Grijpma D, Ovsianikov A. [2020] Biofabrication. 12(4):045036.

A simple and robust protocol for immunostaining Arabidopsis pollen nuclei.

Borg M, Buendía D, Berger F, Plant Reproduction. 2019 Jan; doi.org/10.1007/s00497-018-00360-7

Human blood vessel organoids as a model of diabetic vasculopathy.

Wimmer RA, Leopoldi A, Aichinger M, Wick N, Hantusch B, Novatchkova M, Taubenschmid J, Hämmerle M, Esk C, Bagley JA, Lindenhofer D, Chen G, Boehm M, Agu CA, Yang F, Fu B, Zuber J, Knoblich JA, Kerjaschki D, Penninger JM, Nature 2019 Jan;565(7740):505-510

Central amygdala circuit dynamics underlying the benzodiazepine anxiolytic effect.

Griessner J, Pasieka M, Böhm V, Grössl F, Kaczanowska J, Pliota P, Kargl D, Werner B, Kaouane N, Strobelt S, Kreitz S, Hess A, Haubensak W, Mol Psychiatry. 2018 Nov 30

Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration.

Gerber T, Murawala P, Knapp D, Masselink W, Schuez M, Hermann S, Gac-Santel M, Nowoshilow S, Kageyama J, Khattak S, Currie JD, Camp JG, Tanaka EM, Treutlein B, Science, 2018 Oct; 362 (6413): eaaq0681

Dorsal tegmental dopamine neurons gate associative learning of fear.

Groessl F, Munsch T, Meis S, Griessner J, Kaczanowska J, Pliota P, Kargl D, Badurek S, Kraitsy K, Rassoulpour A, Zuber J, Lessmann V, Haubensak W, Nat. Neurosci 2018 Jul;21(7):952-62

The axolotl genome and the evolution of key tissue formation regulators.

Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW, Nature, 2018 Feb; 554: 50-55

RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.

Rao S, Sigl V, Wimmer RA, Novatchkova M, Jais A, Wagner G, Handschuh S, Uribesalgo I, Hagelkruys A, Kozieradzki I, Tortola L, Nitsch R, Cronin SJ, Orthofer M, Branstetter D, Canon J, Rossi J, D'Arcangelo M, Botling J, Micke P, Fleur L, Edlund K, Bergqvist M, EkmanS, Lendl T, Popper H, Takayanagi H, Kenner L, Hirsch FR, Dougall W, Penninger JM, Genes Dev. 2017 Oct; 31(20): 2099-2112

BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1.

Hogg SJ, Vervoort SJ, Deswal S, Ott CJ, Li J, Cluse LA, Beavis PA, Darcy PK, Martin BP, Spencer A, Traunbauer AK, Sadovnik I, Bauer K, Valent P, Bradner JE, Zuber J, Shortt J, Johnstone RW, Cell Rep. 2017 Feb; 18(9): 2162-2174

Fast volumetric calcium imaging across multiple cortical layers using sculpted light.

Prevedel R, Verhoef AJ, Pernía-Andrade AJ, Weisenburger S, Huang BS, Nöbauer T, Fernández A, Delcour JE, Golshani P, Baltuska A, Vaziri A, Nat Methods, 2016 Dec; 13(12): 1021-1028