An introduction to bioimage analysis - http://bioimagebook.github.io

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Overview

Introduction to Bioimage Analysis

Jupyter Book Badge License: CC BY 4.0 Twitter

This book tries explain the main ideas of image analysis in a practical and engaging way.

It's written primarily for busy biologists who need to analyze images as part of their work -- but I hope others might find it useful as well.

The core content is based on my earlier handbook Analyzing fluorescence microscopy images with ImageJ (PDF, GitBook). This has been extensively revised, generalized and expanded; the new title reflects the fact that it's no longer entirely focussed on fluorescence images, nor on ImageJ -- although both still play a big role.

The biggest change is that it now exists as an open Jupyter Book. This makes the whole thing more maintainable for me, and interactive for anyone who reads it.

It's a work in progress, and probably always will be, but I hope you find it useful.

You can download the images used in the practical exercises here.

Title image

Comments
  • PDF Layout for the book

    PDF Layout for the book

    Hi, This is not an issue but a question. How do I control the layout for the PDF version of the book? I am asking this because I want to write a book myself. Thank you!

    Best regards, Patrick

    opened by PatMis16 1
  • Add Bio-image Analysis Notebooks link & update sampling theorem credit

    Add Bio-image Analysis Notebooks link & update sampling theorem credit

    • Link to @haesleinhuepf's https://github.com/haesleinhuepf/BioImageAnalysisNotebooks (wonderful stuff I didn't know existed before)
    • Add Vladimir Kotelnikov to the mention of the sampling theorem (see chapter 2 and p445 of 'A biography of the pixel' by Alvy Ray Smith for more details)
    opened by petebankhead 0
  • Update dependencies

    Update dependencies

    This includes move to Jupyter book 0.13.1, which uses Sphinx-Design instead of Sphinx-Panels. As a result, all the question/answer tabs needed to be updated.

    opened by petebankhead 0
  • imagej.js and minor fixes

    imagej.js and minor fixes

    Add imagej.js launch buttons for most practicals - thanks to @oeway and this discussion: https://forum.image.sc/t/open-multiple-images-at-once-in-imagej-js/65974

    Fix link error spotted by @joshmoore at https://github.com/bioimagebook/bioimagebook.github.io/pull/1 (and few others GitHub was hiding with redirects)

    Improve consistency of Question/Answer and Practical/Solution combinations.

    opened by petebankhead 0
  • aicsimageio on Apple Silicon Macs

    aicsimageio on Apple Silicon Macs

    Hey @petebankhead! :wave:

    Really enjoyed reading basically all of the Python sections of the book this morning! I honestly might pass this along to others that are interested in general image handling and not just microscopy image handling. It's a great Python intro to images in general!

    On the file formats and dimensions and metadata section, I think you were having issues with installing aicsimageio on Apple Silicon; I am wondering when the last time you tried installing was because a couple of recent patches should have ironed out a lot of the issues with installing.

    pip install --upgrade --force-reinstall --no-cache-dir aicsimageio should be a good check?

    If there are still issues please let me know. Would love to get it working for you!

    Thanks again

    opened by evamaxfield 5
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Bioimage Book
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