Table 3.

Comparison table between advantages, disadvantages, and the used programming language for development of different open-source microscopy viewers, namely QuPath, orbit, ImageJ/Fiji, and napari

Viewer	Advantages	Disadvantages	Language	Operating system	WSI support
QuPath	Good user interface Easy learning curve Many machine learning tools already integrated Native support for WSI	Limited number of plugins Little support for major deep-learning libraries	Java	macOS, Windows, Linux	Yes
ImageJ/Fiji	Good community with quick support High number of plugins Already in use by many research labs	Steep learning curve Rather technical setup Different plugins are required for many processing steps	Java	macOS, Windows, Linux	Plugin required
Orbit	Integration with many server architectures Specifically designed for WSI Many machine learning tools already integrated	Limited number of plugins Smaller community than alternatives	Java	macOS, Windows, Linux	Yes
napari	Good user interface Integration with all scientific Python frameworks and libraries Easy to develop own workflows	Very young project Smaller community, although growing Still under active development for the first stable release	Python	macOS, Windows, Linux	Plugin required
BioImageXD	Many native functions for common image processing steps implemented from well validated frameworks	Less community support than other viewers Less intuitive user interface	Python, C++	macOS, Windows, Linux	Yes
Cytomine	Web-based, zero footprint viewer Very intuitive user interface Good for teaching and interaction	Only web-based client Data has to be uploaded which could lead to privacy issues	Java	Web based	Yes
Icy	Many advanced computer vision functionalities Graphical workflow design editor Great visualization capabilities	Little native machine learning support Designed for researchers with some programming knowledge	Java	MacOS, Windows, Linux	Yes
Cellprofiler	Easy to create whole processing pipelines Automatic processing of large number of images Interation with Cell profiler Analysis for data analysis	Slow at large image files Limited customizability	Python	macOS, Windows	No

This list is not exhaustive but provides an overview about the different arguments a research department might consider when choosing a software for building image analysis workflows. Different requirements have different solutions, where each of the viewer software solutions was built with different intentions.

WSI, whole slide image.