Introduction to Bioimage Analysis using QuPath

Date: Feb 10th 2025
Time: 9:30am - 5.30pm
Location: HMS, Longwood (In-person)
Cost: See Below

About

The Image Analysis Collaboratory is running a workshop over one full day: Introduction to Bioimage Analysis using QuPath.

Participation will be limited to ~20 people. The format will be a combination of tutorials and hands-on exercises inspired by research questions we worked on.

Selection: Mostly based on your short motivation. In case of oversubscription, the available spaces will be distributed evenly between labs and departments.

Note: Participation to the full day is required, if you can only make it one of the days, please apply for the next workshop.

Requirements

This workshop is tailored for beginners. If you already have advanced experience, such as coding your own workflows, this workshop may not be the right fit for your skill level. You need a laptop with admin privileges and interest in learning some bioimage analysis.

Scope

  • to digital image analysis, w. focus on bio-images
  • Introduction to QuPath: general concepts (image handling, project structure, user-interface)
  • Cell detection and segmentation (threshold-, and machine learning-based)
  • Measurements and cell classification (threshold-, and machine learning-based)
  • Tissue detection
  • Density maps and spatial measurements
  • Advanced topics (scripts, batch process)

    • Cost

    Harvard Medical School Quad A Labs : Free of Charge
    Harvard Medical School & Affiliates: $200
    Harvard University: $200
    External: $400

    Eligibility and Billing

    Eligible individuals include internal HMS researchers, HMS affiliates, and external researchers. Payments will be processed through the PPMS System and the information required for system setup and billing is collected only from those accepted to the workshop. Billing occurs monthly, and you will be invoiced within the month following the workshop. Payment for internal HMS participants will be processed via a 33-digit code, payment for external participants can be made by PO or credit card through an electronic invoice generated by the PPMS system. Payment is due within 30 days from the invoice date. A no-show fee equivalent to the full registration cost will be charged for cancellations or no-shows with less than 48 hours notice (excluding weekends and holidays).

    Apply by January 31st 2025 @ 10am
    Some Feedback from Previous Participants

    It was perfect! I learned a lot and Antoine and the group make an amazing effort to do it very easy to follow. Congrats to the team!"

    Incredibly happy with the course - gave me so many ideas and I can't wait to apply what I learned to my own data. Thanks so much!"

    Thanks so much for setting up this workshop! I'm much more confident in analyzing my data, which would not be possible without this workshop. You guys are amazing!"

    Instructors are very well prepared and communicate in a easy and friendly way. Thanks Antoine in special."


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