Molecular Imaging Center (MIC)

1-day workshop in basic image processing with Fiji and QuPath.

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This one-day workshop will introduce two of the most useful image analysis software being used for light microscopy images, Fiji (ImageJ) and QuPath. Both are free to download and are frequently used by scientists worldwide. If you learn how to navigate these powerful tools early in your scientific imaging career, you will have a great advantage in pursuing everything from simple image processing tasks to complex analysis of larger data sets.

Fiji is a version of ImageJ, bundling the plugins needed for scientific image analysis. In most cases, it can directly open proprietary files from different microscopy manufactures, which also means that the essential meta data information follows the images. The most common image processing is accessible, and a skilled person can build complex analysis workflows. It is also possible to make your own macros for more efficient repetition of the workflows. However, to get you started, it is necessary to have some basic knowledge on which information an image actually contains. In this workshop we aim to level up your understanding of an image, take you through some useful image processing steps in addition to some simple analysis.

QuPath is designed to handle larger images typically produced by slide scanners. It filled a gap where Fiji struggled and has evolved to become a very useful analysis tool particularly for light microcopy images of histology samples. It can also handle fluorescent images but with certain limitations (that Fiji takes care of). We will introduce you to some possibilities that QuPath offers and show the difference in handling histology color images compared to fluorescent images.

Program 21.06.2023:

0900-1000:  Presentation: What can we extract from an image and how to digest it?

1015-1230: Workshop 1: Tour of Fiji – you bring your own laptop with Fiji already installed, and we will do things together.

1230-1315: Lunch break.

1315-1530: Workshop 2: Walk the QuPath – you bring your own laptop with QuPath already installed, and we will do things together.

1530-1600: Wrap up.