Welcome to BAB3

We hope you enjoy this course! This book will populate with content as we move through the course.

Here is our agenda for the week!

Please note - while we know many excellent commercial software options exist, we have chosen to focus on open-source, free tools that you can access at home without any paid software license. Bioimage analysis has a tremendously large, friendly, and robust community for making such software tools - you can explore many such tools (or just post, “here’s my picture, here’s my question, what is the right tool to use?”) at the Scientific Community Image Forum - https://forum.image.sc. Some tools are best for large data (where “large” is many voxels, like lightsheet), some are best for large data (where “large” is many small images from something like a plate-scanning microscope); some are best for creating reusable, reproducible pipelines, and some best for interactive exploration.

Does posting on a public forum sound scary?

The image.sc forum LOVES beginners; in fact, it was designed to be helpful for beginners! If you aren’t ready to post, there are tens of thousands of posts available for you to read; real names aren’t required, nor are real descriptions of your biology (if you just say “I want to see the nuclei are positive for marker X”, no one will mind if you don’t tell us what marker X is!). As long as you’re excited to learn, we’re excited to help you!

If you find the possible number of tools to start from overwhelming, you aren’t alone! We have curated some recommendations in the Bioimaging Guide that we think you may find helpful. Certainly also reading the manual for a given tool is a great way to learn more! By the end of this week, you will hopefully be confident in assessing a tool and seeing if it might fit your needs or not.

The links below will populate as we work our way through the course.

Day	Title	Link
Monday	Welcome	Slides
	Participant Intro	Slides
	Intro to Images and Workflows	Slides
	ImageJ	Slides / Exercise
	Intro to Thinking About Images	Slides
	Thinking About Images	Exercise
	Intro to Piximi	Slides
	Manual Annotation in Piximi	Exercise
Tuesday	Classical Segmentation	Slides
	Intro to CellProfiler	Exercise
	Thinking About Measurements	Slides
	Advanced Segmentation in CellProfiler	Exercise
	Classical Machine Learning	Slides
	CellProfiler Analyst	Exercise
Wednesday	Pitfalls in Classic Machine Learning/Intro to Ilastik	Slides
	Ilastik	Exercise
	Intro to QuPath	Slides
	QuPath	Exercise
	Intro to Colocalization	Slides
	The CoLoc Game	Slides / Game Website
Thursday	Command Line, Environments, and Containers	Slides
	Containerized Plugins in CellProfiler	Exercise
	Fiji Macros	Slides / Demo Images and Macro
	Intro to Deep Learning	Slides
	Tensorflow Playground	Exercise
	Intro to Napari	Slides
	MicroSAM in Napari	Slides / Exercise
Friday	Intro to Cellpose	Slides
	Train Your Own Cellpose	Exercise
	BioImaging North America	Slides
	Community Resources	Slides
	Personal Project Playtime	Slides
	Wrapup	Slides