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General Information

CellProfiler is free, open-source software for quantitative analysis of biological images. It is designed for biologists and no prior experience in programming or computer vision is required. In this workshop you will:

• Load an example CellProfiler pipeline, a series of image-processing modules
• Adjust the settings to measure the phenotypes of interest in your images
• Process images automatically — even millions
• Export your data to a spreadsheet or database
• Explore your data and classify complex or subtle phenotypes using machine learning in CellProfiler Analyst

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

When: Aug 30-31, 2022. Add to your Google Calendar.

Requirements: Participants must bring a laptop 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 taryn.dooms@jax.org for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

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Survey

Please be sure to complete this survey after the workshop.

Post-workshop Survey

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Schedule

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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.

Install CellProfiler

Download CellProfiler for Mac or Windows and ask the IT help desk for assistance with installation.

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:

• Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
• Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
• Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

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