_quarto_EN_pdf.yml

project:
  type: book
  output-dir: _pdf_EN
  resources:
    - "CITATION.cff"
    - images
    - screenshots
    - files
    - "script.js"
    - "webpages.js"
    - "webpages.txt"
    - "headerEN.html"


execute:
  freeze: auto

lang: en

book:
  title: "Histopathology Atlas"
  subtitle: "Atlas of Pathology with Whole Slide Images"
  author:
   - name: "Serdar Balcı"
     url: "https://www.serdarbalci.com"
     affiliation: "Memorial Pathology"
     affiliation-url: "https://patoloji.memorial.com.tr/"
     orcid: "0000-0002-7852-3851"
   - name: Pathologists, Assistants and Technicians
     affiliation: "Memorial Pathology & Other Institutions"
     affiliation-url: "https://www.histopathologyatlas.com/authors.html"
  description: |
    Atlas of Pathology with Whole Slide Images
    Histopathology Atlas and Notes for Medical Students
    Atlas of Histopathology
    Notes for Pathology
    Virtual Microscope
    Virtual Microscopy
    Pathology Lecture Notes and Histopathology Atlas is being prepared from Memorial Pathology Archive and collaborators from other institutions.
  abstract: |
    Atlas of Pathology with Whole Slide Images
    Histopathology Atlas and Notes for Medical Students
    Pathology Lecture Notes and Histopathology Atlas is being prepared from Memorial Pathology Archive and collaborators from other institutions.
    If you want to contribute, please [contact us](https://www.patolojiatlasi.com/contributions.html).
  date: last-modified
  image: images/coverEN.png
  output-file: "HistoPathology-Atlas"
  cover-image: images/Histopathology-Atlas-ebook-cover.png
  site-url: https://histopathologyatlas.com/
  search:
    location: navbar
    type: overlay
    copy-button: true
  sidebar:
    style: docked #floating
    background: light
    search: true
    collapsed-level: 1
    pinned: true
  open-graph:
    locale: en_EN
    site-name: Histopathology Atlas
  twitter-card:
    creator: "%40serdarbalci"
    site: "%40patolojinotlari"
  page-navigation: true
  page-footer:
    border: true
    background: light
    left: "Copyright 2022, [patolojiAI](https://www.patolojiai.com/)"
    # right:
    #   - icon: github
    #     href: https://github.com/patolojiatlasi
    #     target: _blank
    #   - icon: github
    #     href: https://github.com/pathologyatlas
    #     target: _blank
    #   - icon: twitter
    #     href: https://twitter.com/patolojinotlari
    #     target: _blank
    #   - icon: globe2
    #     href: https://www.patolojinotlari.com
    #     target: _blank
    #   - icon: globe2
    #     href: https://www.serdarbalci.com
    #     target: _blank

  chapters:
    - text: "Home Page"
      href: index.qmd
    - text: "Introduction"
      href: introduction_pdf_EN.qmd
    - part: "---"
    - part: "General Pathology"
      chapters:
        - text: "Techniques Used in Pathology"
          href: techniques_pdf_EN.qmd
        # - text: "Intracellular Accumulations"
        #   href: intracellular-accumulations_pdf_EN.qmd
#         - text: "Extracellular Accumulations"
#           href: extracellular-accumulations_pdf_EN.qmd
#         - text: "Cellular Injury"
#           href: cell-injury_pdf_EN.qmd
# #         - text: "Hemodynamic Disorders"
# #           href: hemodinamik-bozukluklar_pdf_EN.qmd
#         - text: "Ischemia and Necrosis"
#           href: ischemia-necrosis_pdf_EN.qmd
#         - text: "Congestion"
#           href: congestion_pdf_EN.qmd
#         # - text: "Inflammation"
#         #   href: inflamasyon_pdf_EN.qmd
#         - text: "Amyloidosis"
#           href: amyloidosis_pdf_EN.qmd
#         - text: "Repair Mechanisms"
#           href: repair_pdf_EN.qmd
#         - text: "Erosion"
#           href: erosion_pdf_EN.qmd
    # - part: "Inflamation"
    #   chapters:
    #     - text: "Acute inflammation"
    #       href: acute-inflammation_pdf_EN.qmd
    #     - text: "Chronic inflammation"
    #       href: chronic-inflammation_pdf_EN.qmd
    #     - text: "Granulamatous inflammation"
    #       href: granulamatous-inflammation_pdf_EN.qmd
        # - inflamasyon_pdf_EN.qmd
#     - part: "Infectious Diseases"
#       chapters:
#         - text: "Viruses"
#           href: virus_pdf_EN.qmd
#         - text: "Bacteria"
#           href: bacteria_pdf_EN.qmd
#         - text: "Fungi"
#           href: fungi_pdf_EN.qmd
#         - text: "Parasites"
#           href: parasites_pdf_EN.qmd
#     - part: "Neoplasia, Tumor Pathology Basics"
#       chapters:
#         - text: "Benign Tumors"
#           href: benign_pdf_EN.qmd
#         - text: "Hamartoma"
#           href: hamartoma_pdf_EN.qmd
#         - text: "Heterotopia"
#           href: heterotopia_pdf_EN.qmd
#         - text: "Metaplasia"
#           href: metaplasia_pdf_EN.qmd
#         - text: "Carcinogenesis"
#           href: carcinogenesis_pdf_EN.qmd
#         - text: "The properties of Malignant Tumors"
#           href: malignant_pdf_EN.qmd
#         - text: "Metastasis"
#           href: metastasis_pdf_EN.qmd
#         - text: "Tumor Spread to Other Organs"
#           href: tumor-spread_pdf_EN.qmd
#     - part: "Prognostic Morphologic Features of Neoplasms"
#       chapters:
#         - text: "Venous Invasion"
#           href: venous-invasion_pdf_EN.qmd
#         - text: "Extramural Venous Invaasion"
#           href: extramural-venous-invasion_pdf_EN.qmd
#     - part: "Hematopathology"
#       chapters:
# #        - hematopatoloji_pdf_EN.qmd
#         - text: "Hodgkin Lymphoma"
#           href: hodgkin_pdf_EN.qmd
#     - part: "Gastrointestinal System"
#       chapters:
#         - gastro_pdf_EN.qmd
#         - text: "Esophagus"
#           href: esophagus_pdf_EN.qmd
#         - text: "Stomach"
#           href: stomach_pdf_EN.qmd
#         - text: "Gastritis"
#           href: gastritis_pdf_EN.qmd
#         - text: "Duodenum"
#           href: duodenum_pdf_EN.qmd
#         - text: "Colon"
#           href: colon_pdf_EN.qmd
#         - text: "Crohn's Disease"
#           href: crohn_pdf_EN.qmd
#     - part: "Liver"
#       chapters:
#         - text: "Liver Tumors"
#           href: liver_pdf_EN.qmd
#         - text: "Benign Liver Tumors"
#           href: benign-liver-tumors_pdf_EN.qmd
#     - part: "Pancreatobiliary system"
#       chapters:
#         - text: "Pancreas"
#           href: pancreas_pdf_EN.qmd
#         - text: "Pancreas Ductal Adenocarcinoma"
#           href: pdac_pdf_EN.qmd
#         - text: "Gallbladder"
#           href: gallbladder_pdf_EN.qmd
#         - text: "Ampulla of Vater"
#           href: ampulla-vater_pdf_EN.qmd
#     - part: "Lung"
#       chapters:
#         - text: "Neuroendocrine"
#           href: neuroendocrine_pdf_EN.qmd
#     - part: "Mezotel"
#       chapters:
#         - text: "Abdomen"
#           href: mesothelial_pdf_EN.qmd
#     - part: "Gynecopathology"
#       chapters:
#         - text: "Gynecopathology"
#           href: gynecologic_pdf_EN.qmd
#         - text: "Genital System"
#           href: genital_pdf_EN.qmd
#         - text: "Cervix"
#           href: cervix_pdf_EN.qmd
#         - text: "Endometrium"
#           href: endometrium_pdf_EN.qmd
#         - text: "Endometriosis"
#           href: endometriosis_pdf_EN.qmd
#     - part: "Uropathology"
#       chapters:
#         - text: "Uropathology"
#           href: urinary_pdf_EN.qmd
#         - text: "Kidney Tumors / Renal Tumors"
#           href: kidney_pdf_EN.qmd
#         - text: "Prostate"
#           href: prostate_pdf_EN.qmd
#     - part: "Endocrine System"
#       chapters:
#         - text: "Pituitary Adenoma"
#           href: pituitary_pdf_EN.qmd
#     # - part: "Breast"
#     #   chapters:
#     #     - text: "Breast Tumors"
#     #       href: meme.md
#     - part: "Head and Neck"
#       chapters:
#         - text: "Nasopharynx"
#           href: nasopharynx_pdf_EN.qmd
#         - text: "Ear"
#           href: ear_pdf_EN.qmd
#         - text: "Salivary Gland"
#           href: salivary_pdf_EN.qmd
#     - part: "Central Nervous System"
#       chapters:
#         - text: "Glioma"
#           href: glioma_pdf_EN.qmd
#         - text: "Meningioma"
#           href: meningioma_pdf_EN.qmd
#         - text: "Vascular Lesions"
#           href: cns-vascular_pdf_EN.qmd
#     - part: "Bone"
#       chapters:
#         - text: "Bone Tumors"
#           href: bone_pdf_EN.qmd
#     - part: "Soft Tissue"
#       chapters:
#         - text: "Adipose Tissue"
#           href: adipose_pdf_EN.qmd
#     - part: "Pediatric and Perinatal"
#       chapters:
#         - text: "Placenta"
#           href: placenta_pdf_EN.qmd
#     - part: "---"
#     - part: "Special Collections"
#       chapters:
#         - text: "GBDAtlas"
#           href: gbd_pdf_EN.qmd
#         - text: "Hacettepe Case of Month"
#           href: hacettepecom_pdf_EN.qmd
#         - text: "BSAtlas"
#           href: bs_pdf_EN.qmd
#         - text: "ICEtlas"
#           href: ice_pdf_EN.qmd
#         - text: "Similar Websites"
#           href: wsi_pdf_EN.qmd
    - part: "---"
    - references_pdf_EN.qmd
    - part: "---"
  appendices:
    - text: "Authors and Contributors"
      href: authors_pdf_EN.qmd
    # - yonetim-gelistirme.md
    - text: "Contributions are welcome"
      href: contributions_pdf_EN.qmd
    - text: "Comments are welcome"
      href: comments_pdf_EN.qmd
    # - text: "List"
    #   href: listing_pdf_EN.qmd
    # - listing2_pdf_EN.qmd



format:
  pdf:
    toc: true
    toc-depth: 2
    # lof: true
    # lot: true
    number-sections: true
    number-depth: 2
    colorlinks: true
    keep-tex: true
    # include-in-header:
    #   text: |
    #     \usepackage{makeidx}
    #     \makeindex
#         \usepackage{fvextra}
#         \DefineVerbatimEnvironment{Highlighting}{Verbatim}{breaklines,commandchars=\\\{\}}
#         \areaset[0.50in]{4.5in}{8in}
#         \usepackage{titlesec}
#         \usepackage{svg}
#         \usepackage{transparent}
#         \usepackage{tikzfill}
#         \usepackage{sidenotes}
#         \usepackage{marginnote}
#         \usepackage{changepage}
#     include-before-body:
#       text: |
#         \RecustomVerbatimEnvironment{verbatim}{Verbatim}{
#            showspaces = false,
#            showtabs = false,
#            breaksymbolleft={},
#            breaklines
#            % Note: setting commandchars=\\\{\} here will cause an error
#         }
    # include-after-body:
    #   text: |
    #     \printindex
    execute:
      warning: false

#    # documentclass: scrbook
#    # classoption: [paper=6in:9in,pagesize=pdftex,headinclude=on,footinclude=on,12pt]


# https://quarto.org/docs/reference/formats/pdf.html


citation:
    type: webpage
    container-title: Patoloji Atlası
    url: "https://www.histopathologyatlas.com/"


editor: source