_toc.yml

format: jb-book
root: index
parts:
- caption: teamtomo.org
  chapters:
  - file: teamtomo/about
  - file: teamtomo/contributing/index
    sections:
    - file: teamtomo/contributing/git_guide
    - file: teamtomo/contributing/screen-capture
    - file: teamtomo/contributing/wishlist
- caption: Theory
  chapters:
  - file: theory/cryo-et/index
    sections:
    - file: theory/cryo-et/tilt-schemes
    - file: theory/cryo-et/tilt-series-alignment
  - file: theory/subtomogram-averaging/index
    sections:
    - file: theory/subtomogram-averaging/preprocessing/index
    - file: theory/subtomogram-averaging/particle-picking/index
      sections:
      - file: theory/subtomogram-averaging/particle-picking/template-matching
      - file: theory/subtomogram-averaging/particle-picking/geometrical-supports
      - file: theory/subtomogram-averaging/particle-picking/subboxing
    - file: theory/subtomogram-averaging/refinement/index
  - file: theory/image-processing/introduction
- caption: Walkthroughs
  chapters:
  - file: walkthroughs/EMPIAR-10164/introduction
    title: EMPIAR-10164 (HIV VLPs)
    sections:
    - file: walkthroughs/EMPIAR-10164/preparation
    - file: walkthroughs/EMPIAR-10164/2d-preprocessing
    - file: walkthroughs/EMPIAR-10164/tilt-series-to-tomograms
    - file: walkthroughs/EMPIAR-10164/geometrical-picking
    - file: walkthroughs/EMPIAR-10164/ini-model
    - file: walkthroughs/EMPIAR-10164/particle-picking
    - file: walkthroughs/EMPIAR-10164/relion
    - file: walkthroughs/EMPIAR-10164/m
- caption: mini-tutorials
  chapters:
  - file: mini-tutorials/dynamo/index
    sections:
    - file: mini-tutorials/dynamo/simple-alignment
    - file: mini-tutorials/dynamo/extract-from-catalogue
    - file: mini-tutorials/dynamo/dipoles-to-vesicles
    - file: mini-tutorials/dynamo/dtmslice-controls
    - file: mini-tutorials/dynamo/interactive-mask-creation
- caption: computing
  chapters:
  - file: computing/python/index
    sections:
    - file: computing/python/getting-started
    - file: computing/python/virtual-environments
    - file: computing/python/useful-packages/useful-packages
      sections:
      - file: computing/python/useful-packages/dynamotable
      - file: computing/python/useful-packages/emfile
      - file: computing/python/useful-packages/eulerangles
      - file: computing/python/useful-packages/mrcfile
      - file: computing/python/useful-packages/napari
      - file: computing/python/useful-packages/starfile
  - file: computing/matlab/index
    sections:
    - file: computing/matlab/add-to-path
- caption: Resources
  chapters:
  - file: resources/literature/index
    sections:
    - file: resources/literature/protocols/protocols
    - file: resources/literature/reviews/reviews
      sections:
      - file: resources/literature/reviews/schur19
      - file: resources/literature/reviews/lucic08
      - file: resources/literature/reviews/lucic05
    - file: resources/literature/book-chapters/book-chapters
      sections:
      - file: resources/literature/book-chapters/subtomo-leigh19
      - file: resources/literature/book-chapters/cryo-et-sta-wan16
      - file: resources/literature/book-chapters/fiducial-alignments-mastronarde07
  - file: resources/cryoet-software/cryoet-software
    sections:
    - file: resources/cryoet-software/appion-protomo/appion-protomo
    - file: resources/cryoet-software/cryolo/cryolo
    - file: resources/cryoet-software/dynamo/dynamo
      sections:
      - file: resources/cryoet-software/dynamo/starters-guide
      - file: resources/cryoet-software/dynamo/advanced-starters-guide
      - file: resources/cryoet-software/dynamo/tilt-series-alignment
      - file: resources/cryoet-software/dynamo/PCA
    - file: resources/cryoet-software/eman2/eman2
      sections:
      - file: resources/cryoet-software/eman2/full-tutorial
      - file: resources/cryoet-software/eman2/segmentation
    - file: resources/cryoet-software/emclarity/emclarity
      sections:
      - file: resources/cryoet-software/emclarity/tutorial
    - file: resources/cryoet-software/imod/imod
      sections:
      - file: resources/cryoet-software/imod/tomo-guide
      - file: resources/cryoet-software/imod/etomo-fiducial-tuto
      - file: resources/cryoet-software/imod/etomo-patch-track-tuto
      - file: resources/cryoet-software/imod/batch-alignment
    - file: resources/cryoet-software/m/m
      sections:
      - file: resources/cryoet-software/m/user-guide
    - file: resources/cryoet-software/novactf/novactf
    - file: resources/cryoet-software/novasta/novasta
    - file: resources/cryoet-software/peet/peet
    - file: resources/cryoet-software/pytom/pytom
    - file: resources/cryoet-software/relion/relion
    - file: resources/cryoet-software/stopgap/stopgap
    - file: resources/cryoet-software/topaz_denoise_3d/topaz_denoise_3d
    - file: resources/cryoet-software/warp/warp
      sections:
      - file: resources/cryoet-software/warp/user-guide