Tag Archives: digital pathology

Application of ICC profiles to digital pathology images

Background on Color Calibration

Digital whole slide image scanners are designed to take stained tissue on glass slides and digitize them into bytes for usage in the digital world. The process by which slide scanners perform this operation does not produce a perfect digital equivalent of the original slide as the hardware involved (led/blub, camera sensor, quantizer) can introduce some biases during the sampling process. For example, different camera sensors may detect colors with different levels of specificity/accuracy/density, resulting in similar but not perfect representations of the associated real-world subjects.

Concretely, there is often a difference between the color you perceive in the real-world under a microscope versus what you would see if you looked at the corresponding digital copy of the same slide. This blog post discusses how to correct for this discrepancy using ICC profiles.

Continue reading Application of ICC profiles to digital pathology images

Using Paquo to directly interact with QuPath project files for usage in digital pathology machine learning

This is an updated version of the previously described workflow on how to load and classify annotations/detections created in QuPath for usage in downstream machine learning workflows. The original post described how to use the Groovy programming language used by QuPath to export annotations/detections as GeoJSON from within QuPath, made use of a Python script to classify them, and lastly used another Groovy script to reimport them. If you are not familiar with QuPath and/or its annotations you should probably read the original post first to provide better context and understanding of the respective workflows, as well as being able to appreciate the more elegant approach taken here. If you are already using the described approach, you should be able to easily modify it to follow this newer approach.

Continue reading Using Paquo to directly interact with QuPath project files for usage in digital pathology machine learning

Tutorial: Quick Annotator for Tubule Segmentation

The manual labeling of large numbers of objects is a frequent occurrence when training deep learning classifiers in the digital histopathology domain. Often this can become extremely tedious and potentially even insurmountable.

To aid people in this annotation process we have developed and released Quick Annotator (QA), a tool which employs a deep learning backend to simultaneously learn and aid the user in the annotation process. A pre-print explaining this tool in more detail is available [here].

Continue reading Tutorial: Quick Annotator for Tubule Segmentation

The noise in our digital pathology slides

In adding new features to HistoQC , I stumbled upon a very interesting insight that I thought I would take a moment to share. The amount of noise and artifacts in digital pathology (DP) whole slide images (WSI) is far more extensive than I had previously thought.

Continue reading The noise in our digital pathology slides