/
_toc.yml
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/
_toc.yml
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format: jb-book
root: index
defaults:
caption: Default Caption # See https://github.com/executablebooks/jupyter-book/issues/2009
parts:
- caption: Front matter
chapters:
- file: chapters/0-preamble/acknowledgements/acknowledgements
- file: chapters/0-preamble/license
- file: chapters/0-preamble/disclaimer
- file: CHANGELOG.md
- caption: Before we begin
chapters:
- file: chapters/0-preamble/preface/preface
- file: chapters/0-preamble/reading/reading
- caption: Introducing images
chapters:
- file: chapters/1-concepts/1-images_and_pixels/images_and_pixels
sections:
- file: chapters/1-concepts/1-images_and_pixels/imagej
- file: chapters/1-concepts/1-images_and_pixels/python
- file: chapters/1-concepts/2-measurements/measurements
sections:
- file: chapters/1-concepts/2-measurements/imagej
- file: chapters/1-concepts/2-measurements/python
- file: chapters/1-concepts/3-bit_depths/bit_depths
sections:
- file: chapters/1-concepts/3-bit_depths/imagej
- file: chapters/1-concepts/3-bit_depths/python
- file: chapters/1-concepts/4-colors/colors
sections:
- file: chapters/1-concepts/4-colors/imagej
- file: chapters/1-concepts/4-colors/python
- file: chapters/1-concepts/5-pixel_size/pixel_size
sections:
- file: chapters/1-concepts/5-pixel_size/imagej
- file: chapters/1-concepts/5-pixel_size/python
- file: chapters/1-concepts/6-files/files
sections:
- file: chapters/1-concepts/6-files/imagej
- file: chapters/1-concepts/6-files/python
- caption: Processing & analysis
chapters:
- file: chapters/2-processing/1-processing_and_analysis/processing_and_analysis
- file: chapters/2-processing/2-point_operations/point_operations
sections:
- file: chapters/2-processing/2-point_operations/imagej
# - file: chapters/2-processing/2-point_operations/python
- file: chapters/2-processing/3-thresholding/thresholding
sections:
- file: chapters/2-processing/3-thresholding/imagej
# - file: chapters/2-processing/3-thresholding/python
- file: chapters/2-processing/4-filters/filters
sections:
- file: chapters/2-processing/4-filters/imagej
# - file: chapters/2-processing/4-filters/python
- file: chapters/2-processing/5-morph/morph
sections:
- file: chapters/2-processing/5-morph/imagej
# - file: chapters/2-processing/5-morph/python
- file: chapters/2-processing/6-transforms/transforms
sections:
- file: chapters/2-processing/6-transforms/imagej
# - file: chapters/2-processing/6-transforms/python
- file: chapters/2-processing/7-multidimensional_processing/multidimensional_processing
sections:
- file: chapters/2-processing/7-multidimensional_processing/imagej
# - file: chapters/2-processing/7-multidimensional_processing/python
- caption: Fluorescence microscopy
chapters:
- file: chapters/3-fluorescence/1-formation_overview/formation_overview
- file: chapters/3-fluorescence/2-formation_spatial/formation_spatial
- file: chapters/3-fluorescence/3-formation_noise/formation_noise
- file: chapters/3-fluorescence/4-microscope_types/microscope_types
- caption: Appendices
chapters:
- file: chapters/appendices/next_steps/next_steps
- file: chapters/appendices/python/python
- file: chapters/appendices/macros/macro_intro
sections:
- file: chapters/appendices/macros/macro_dog
- file: chapters/appendices/macros/macro_simulating