QuPath: Quantitative Pathology & Bioimage Analysis

The Jackson Laboratory

Online

Nov 9, 16 & 23, 2021

8:30 am - 12:30 pm EDT

Instructors: Melvin Gelbard, Erick Ratamero

Helpers:

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General Information

QuPath is cross-platform, user-friendly open source software for digital pathology and whole slide image analysis. Features include annotating and viewing images (including whole slide and microscopy), workflows for brightfield and fluorescence, tasks like cell segmentation and microarray dearraying, and machine learning for classification. QuPath has also been designed to be developer-friendly, and combines an extensible design with powerful scripting tools.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Nov 9, 16 & 23, 2021. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email susan.mcclatchy@jax.org or erick.ratamero@jax.org for more information.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.


Surveys

Please be sure to complete these surveys before and after the workshop.

Post-workshop Survey


Schedule


Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.