dogsled 0.0.1

Medical slide normalisation

dogsled is an open-source Python package that does only one thing: Macenko [1] stain normalisation of large medical slides readable by OpenSlide. It generates either JPEG or TIFF normalised image

Why dogsled? Well, first of all, because of the dogs. Second, because together many dogs can push a cargo too heavy for one dog to handle. Similarily, dogsled divides heavy computations into smaller ones. As with many algorithms and life situations, divide and conquer, right?

Quirks and features

Currently, dogsled can:

• normalise all slides located in a specified folder
• normalise slides specified by name
• normalise slides defined in a QuPath library (either all or the ones specified by name and/or index)
• generate JPEG equivalents of the normalised slides
• generate TIFF equivalents of the normalised slides (also for large slides not fitting in RAM)
• create hematoxylin/eosin decoupled normalised images
• create thumbnails of all slides (pre-normalised and normalised)

Documentation

dogsled about page, quickstart, installation and API can be found at dogsled.readthedocs.io

[1] M. Macenko, M. Niethammer, J. S. Marron, D. Borland, J. T. Woosley, Guan Xiaojun, C. Schmitt, and N. E. Thomas. A method for normalizing histology slides for quantitative analysis. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1107–1110. 2009. doi:10.1109/ISBI.2009.5193250.