20. December 2017


Orbit reference publication (preprint)

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

So far please use the preprint https://doi.org/10.1101/731000

Manuel Stritt, Anna K. Stalder, Enrico Vezzali: Orbit Image Analysis: An open-source whole slide image analysis tool, bioRxiv, 2019, doi = {10.1101/731000}


@article {Stritt731000, 
author = {Stritt, Manuel and Stalder, Anna K. and Vezzali, Enrico},
title = {Orbit Image Analysis: An open-source whole slide image analysis tool},
elocation-id = {731000},
year = {2019},
doi = {10.1101/731000},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2019/08/09/731000},
eprint = {https://www.biorxiv.org/content/early/2019/08/09/731000.full.pdf},
journal = {bioRxiv}