20. December 2017


Orbit reference publication

Orbit use-cases

  • Douglas, A., S. Fitzgerald, A. Pandit, and K. M. Doyle. “Storage of blood clots for histological analysis: How long is too long in saline and paraformaldehyde?.” Histology and histopathology (2019): 18154-18154. https://doi.org/10.14670/HH-18-154
  • Fitzgerald, Seán, Shunli Wang, Daying Dai, Dennis Murphree, Abhay Pandit, Andrew Douglas, Ramanathan Kadirvel, Waleed Brinjikji, David F. Kallmes, and Karen M. Doyle. “Machine-Learned Characterization of Acute Ischemic Stroke Clots Reveals a Correlation Between Clot Composition and HU Density on CT.” (2018) PDF
  • Strasser, Daniel S., Shanon Seger, Christian Bussmann, Gabin M. Pierlot, Peter MA Groenen, Anna K. Stalder, and Alex Straumann. “Eosinophilic oesophagitis: relevance of mast cell infiltration.” Histopathology 73, no. 3 (2018): 454-463. https://onlinelibrary.wiley.com/doi/full/10.1111/his.13653
  • Shanon Seger, Manuel Stritt, Enrico Vezzali, Oliver Nayler, Patrick Hess, Peter MA Groenen, and Anna K. Stalder:
    A fully automated image analysis method to quantify lung fibrosis in the bleomycin-induced  rat model. PlosOne, 2018, DOI.
    Supplementary Material: Orbit Model for quantification.
  • Shanon Seger, Manuel Stritt, Kathrin Doppler, Stephan Frank, Adrian Panaite, Thierry Kuntzer, Andreas Steck, Axel Pagenstecher, Claudia Sommer and Anna K Stalder (2015):
    A semi-automated method to assess intraepidermal nerve fibre density in human skin biopsies, Histopathology. DOI: 10.1111/his.12794
  • Manuel Stritt, Roman Bär, Joël Freyss, Julia Marrie, Enrico Vezzali, Edgar Weber, Anna Stalder (2011):
    Supervised Machine Learning Methods for Quantification of Pulmonary Fibrosis, 6th International Conference on Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry (MDA 2011), New York, August 2011, ibai-publishing. [pdf]

Nice article about Orbit

How to cite Orbit

Please cite our main publication:

Stritt M, Stalder AK, Vezzali E (2020) Orbit Image Analysis: An open-source whole slide image analysis tool. PLoS Comput Biol 16(2): e1007313. https://doi.org/10.1371/journal.pcbi.1007313


    author = {Stritt, Manuel AND Stalder, Anna K. AND Vezzali, Enrico},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {Orbit Image Analysis: An open-source whole slide image analysis tool},
    year = {2020},
    month = {02},
    volume = {16},
    url = {https://doi.org/10.1371/journal.pcbi.1007313},
    pages = {1-19},
    number = {2},
    doi = {10.1371/journal.pcbi.1007313}

RIS (e.g. Endnote):

T1  - Orbit Image Analysis: An open-source whole slide image analysis tool
A1  - Stritt, Manuel
A1  - Stalder, Anna K.
A1  - Vezzali, Enrico
Y1  - 2020/02/05
N2  - Author summary Whole slide images (WSI) are digital scans of samples, e.g. tissue sections. It is very convenient to view samples in this digital form, and with the increasing computation power it can also be used for quantification. These images are often too large to be analysed with standard tools. To overcome this issue, we created on open-source tool called Orbit Image Analysis which divides the images into smaller parts and allows the analysis of it with either embedded algorithms or the integration of existing tools. It also provides mechanisms to process huge amounts of images in distributed computing environments, such as clusters or cloud infrastructures. In this paper we describe the Orbit system and demonstrate its application based on three real-word use-cases.
JF  - PLOS Computational Biology
JA  - PLOS Computational Biology
VL  - 16
IS  - 2
UR  - https://doi.org/10.1371/journal.pcbi.1007313
SP  - e1007313
EP  - 
PB  - Public Library of Science
M3  - doi:10.1371/journal.pcbi.1007313
ER  -