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BAB3 (Bioimage Analysis Beginnings Broad Bootcamp) Lab Manual - Home BAB3 (Bioimage Analysis Beginnings Broad Bootcamp) Lab Manual - Home
  • Welcome to BAB3

Labs and Exercises

  • Day 1, Exercise 1: Introduction to Fiji
  • Day 1, Exercise 2: developing image processing intuitions
  • Day 1, Exercise 3: Making Manual Annotations with Piximi
  • Day 2, Exercise 1: Introduction to CellProfiler
  • Day 2, Exercise 2: Advanced Segmentation and Organelle Analysis
  • Day 2, Exercise 3: Classification with CellProfiler Analyst
  • Day 3, Exercise 1: Practical introduction to ilastik
  • Day 3, Exercise 2: Practical introduction to QuPath
  • Day 4, Exercise 1 - Interfacing CellProfiler with other software tools via files and plugins
  • Day 4, Exercise 2 - ‘Segment Anything’ Model (SAM) for Microscopy
  • Day 5, Exercise 1 - Segmenting Data with Cellpose

Additional Resources

  • Downloads
  • Helpful links for now and the future
  • Bibliography
  • .md

Helpful links for now and the future

Contents

  • For finding experts to help you right now
  • Organizations that want to help
  • Places to learn more (or to learn where to learn more)
  • Blog posts you may like

Helpful links for now and the future#

For finding experts to help you right now#

  • Image.sc forum 4 - a centralized forum for >60 open source image analysis tools. Posts from beginners very welcome!

Organizations that want to help#

  • AI4Life

  • The Global Bioimage Analysts’ Society (GloBIAS)

    • Find your local bioimage analyst in GloBIAS’ database

  • The Center for Open Bioimage Analysis (COBA) offers free (though limited) one-on-one consultations with image analysts (among other resources!). You can sign up for their Office Hours.

Places to learn more (or to learn where to learn more)#

  • The BioImaging Guide 5

  • Introduction to Bioimage Analysis (Pete Bankhead)

  • HMS CITE ‘favorite references’

  • Community-developed checklists for publishing images and image analyses 6

  • The Images to Knowledge conference

  • Metrics Reloaded 7,8,9 - an interactive tool for picking the right metric for measuring the accuracy of your imaging-related algorithm (segmentation, classification, etc)

  • Believing is seeing - the deceptive influence of bias in quantitative microscopy 10 - why even quantification is sometimes not enough to make sure your results are unbiased

  • The crucial role of bioimage analysts in scientific research and publication 11 - why bioimage analysis is so important, and how to work with (and support!) your friendly local bioimage analyst.

  • Enabling global image data sharing in the life sciences 12 - why and how should we share our image data when we’re ready to publish it?

  • This awesome online Nobias Advanced Scripting in Fiji Course The course assumes familiarity with Fiji but no coding experience!

Blog posts you may like#

  • How to write a bug report when your favorite software is broken

  • When to say ‘good enough’ in tuning your image analysis

  • Some best practices for beginners at Jupyter Notebook

  • Docker for biologists

  • Using Cellpose and Stardist in CellProfiler

  • “Thinking like an image analyst” blog series - going through the process of solving an image analysis problem. Parts: 1 2 3 4 5

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Downloads

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Bibliography

Contents
  • For finding experts to help you right now
  • Organizations that want to help
  • Places to learn more (or to learn where to learn more)
  • Blog posts you may like

By Broad Institute Imaging Platform

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