template

template for pathology atlas repositories

Completed RGB microscope mosaics can also be prepared with the local sibling Pathology Atlas Pipeline checkout's import_stitched_tiff.py; usage and evidence are in its docs/slideprep-atlas-integration.md. Copy the generated .dzi, matching _files directory (including vips-properties.xml), and .import.json into the case. Keep the original TIFF separately, and check colour, seams, and physical calibration in QuPath before publishing. The import performs no stitching or inpainting.

{{< include ./_subchapters/_template.qmd >}}

see [make-html-WSI](https://github.com/pathologyatlas/make-html-WSI) for more information and [TODO](https://github.com/pathologyatlas/TODO) to add cases

update html file heading:

<title>TemplateEN TemplateTR</title>

<meta name="keywords" content="TemplateEN, TemplateTR, patoloji, atlas, pathology, whole slide image, virtual microscopy, virtual microscope, sanal mikroskop">

<meta name="description" content="TemplateEN TemplateTR">

vips dzsave HE.svs HE

update html file to match .dzi file

consider using git_push.sh script to upload files to github, since the number of generated files is huge

after upload complete, do not forget to activate github pages for the new repository

<title>TemplateEN TemplateTR</title>

https://images.patolojiatlasi.com/template/

https://images.patolojiatlasi.com/template/HE1.html

TemplateTR

Tam Ekran Görmek İçin Resmi Tıklayın

TemplateEN

Click for Full Screen WSI

Mikroskopik görüntüleri inceleyin:

<iframe src="https://images.patolojiatlasi.com/template/HE1.html" style="height:600px;width:100%;" data-external="1"></iframe>

See Microscopy with viewer:

<iframe src="https://images.patolojiatlasi.com/template/HE1.html" style="height:600px;width:100%;" data-external="1"></iframe>

https://images.patolojiatlasi.com/template/

https://images.patolojiatlasi.com/template/HE2.html

TemplateTR

Tam Ekran Görmek İçin Resmi Tıklayın

TemplateEN

Click for Full Screen WSI

Mikroskopik görüntüleri inceleyin:

<iframe src="https://images.patolojiatlasi.com/template/HE2.html" style="height:600px;width:100%;" data-external="1"></iframe>

See Microscopy with viewer:

<iframe src="https://images.patolojiatlasi.com/template/HE2.html" style="height:600px;width:100%;" data-external="1"></iframe>

- stainname: template-HE1
  reponame: template
  titleTR: TemplateTR
  titleEN: TemplateEN
  organTR: ''
  organEN: ''
  speciality: ''
  type: published
  author:
  - Serdar Balci
  - Memorial Patoloji
  date: 2024-03-09
  url: https://images.patolojiatlasi.com/template/HE1.html
  note: ''
  categoriesTR:
  - ''
  - ''
  - ''
  - patoloji
  - atlas
  - histopatoloji
  - whole slide image
  - sanal mikroskop
  categoriesEN:
  - ''
  - ''
  - ''
  - pathology
  - atlas
  - histopathology
  - whole slide image
  - virtual microscopy
  - virtual microscope
  screenshot: https://www.patolojiatlasi.com/screenshots/thumbnail_template-HE1.png
  github: https:///github.com/pathologyatlas/template
  githubpage: https://pathologyatlas.github.io/template
  youtube: https://www.youtube.com/watch?v=youtube_link

- stainname: template-HE2
  reponame: template
  titleTR: TemplateTR
  titleEN: TemplateEN
  organTR: ''
  organEN: ''
  speciality: ''
  type: published
  author:
  - Serdar Balci
  - Memorial Patoloji
  date: 2024-03-09
  url: https://images.patolojiatlasi.com/template/HE2.html
  note: ''
  categoriesTR:
  - ''
  - ''
  - ''
  - patoloji
  - atlas
  - histopatoloji
  - whole slide image
  - sanal mikroskop
  categoriesEN:
  - ''
  - ''
  - ''
  - pathology
  - atlas
  - histopathology
  - whole slide image
  - virtual microscopy
  - virtual microscope
  screenshot: https://www.patolojiatlasi.com/screenshots/thumbnail_template-HE2.png
  github: https:///github.com/pathologyatlas/template
  githubpage: https://pathologyatlas.github.io/template
  youtube: https://www.youtube.com/watch?v=youtube_link

---

• Sosyal medyadan derlenen görüntülerden oluşan patoloji notları için tıklayın.

• For social media based pathology notes click here.

<iframe width="160" height="400" src="https://leanpub.com/patolojiatlasi/embed" frameborder="0" allowtransparency="true"></iframe>

Atıf için (Citation)
Open Science Framework DOI: 10.17605/OSF.IO/6W5K8