PART 1 - Fiji Basics for bioimage analysis: 20-21/09/2017 10:00-18:00;
PART 2 - QuPath for digital pathology analysis: 22/09/2017 10:00-18:00
Driven by an array of new technologies (including high-throughput and high-content approaches in screening, sequencing and imaging), the life sciences are becoming increasingly quantitative. The demand for analysis of complex data sets has boosted the developments and advances of dedicated software tools to process and analyze such data quantitatively using computers.
Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
QuPath, an open source software for Quantitative Pathology, aims to help improve the speed, objectivity and reproducibility of digital pathology analysis and biomarker interpretation by offering an open, powerful, flexible, extensible software platform for whole slide image analysis.
For this, together with the QuPath team, we are organizing a handson workshop (September 20-22) for both beginners and advanced users. The workshop aims at introducing some insights to both tools in tackling image analysis questions.
Poblenou Campus is easily accessible both by public transport: Metro (L1 Glòries, L4 Llacuna), Tram (T4 Ca l’Aranyó, T5 i T6 La Farinera), Train (Clot-Aragó), and Bus (H14, B25, B20, 192, 92, 42, 40, 7, 6). It is also easily accessible by private transport but parking slots are really reduced.
Programme can be found here.
- We will offer computer rooms with both Fiji and QuPath installed already. However, you could also bring your own laptop for this workshop.
- (ONLY for those with own laptops) We suggest to download and install the software packages as well as example data on your own laptop in advance and bring the laptop (64bit!) to the workshop together with your own data (file sizes < 100 MB).
- The work on your own data session is a good opportunity to see what the tools can achieve on your own data.
Some of the workshop photos could be found here!
Speakers and instructors
Pete is a senior image analyst at Philips. Before this, he worked as postdoc in the Bioimaging Informatics group in the Centre for Cancer Research and Cell Biology at Queen’s University in Belfast.
Chong is a computer science engineer and works at SimBioSys group at UPF within the Maria de Maeztu Programme, on medical and bioimage analysis.