New tutorial: Quantitative Analysis of Histological Staining Using Color Deconvolution

topics/imaging/tutorials/stain-quantification-color-deconvolution/data-library.yaml

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+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Imaging
+  description: Bioimaging analysis using Galaxy
+  items:
+  - name: Where to start with bioimage analysis in Galaxy
+    items:
+    - name: 'DOI:'
+      description: latest
+      items:
+      - url: 
+        src: url
+        ext: 
+        info: 

topics/imaging/tutorials/stain-quantification-color-deconvolution/faqs/index.md

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+---
+layout: faq-page
+---

topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.bib

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+@article{Batut2018,
+  doi     = {10.1016/j.cels.2018.05.012},
+  url     = {https://doi.org/10.1016/j.cels.2018.05.012},
+  year    = {2018},
+  month   = jun,
+  publisher = {Elsevier {BV}},
+  volume  = {6},
+  number  = {6},
+  pages   = {752--758.e1},
+  author  = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and
+             Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and
+             Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and
+             Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and
+             Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and
+             Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and
+             Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and
+             Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
+             Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and
+             Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and
+             Dilmurat Yusuf and James Taylor and Rolf Backofen and
+             Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
+  title   = {Community-Driven Data Analysis Training for Biology},
+  journal = {Cell Systems}
+}
+
+@online{gtn-website,
+  author  = {GTN community},
+  title   = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url     = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}
+
+@article{Ruifrok2001,
+  author  = {Ruifrok, Arnout C. and Johnston, Dennis A.},
+  title   = {Quantification of histochemical staining by color deconvolution},
+  journal = {Analytical and Quantitative Cytology and Histology},
+  year    = {2001},
+  volume  = {23},
+  number  = {4},
+  pages   = {291--299},
+  pmid    = {11531144},
+  url     = {https://pubmed.ncbi.nlm.nih.gov/11531144}
+}
+
+@article{Chen2017,
+  author  = {Chen, Ying and Yu, Qi and Xu, Cang-Bao},
+  title   = {A convenient method for quantifying collagen fibers in atherosclerotic lesions by {ImageJ} software},
+  journal = {International Journal of Clinical and Experimental Medicine},
+  year    = {2017},
+  volume  = {10},
+  number  = {10},
+  pages   = {14904--14910},
+  issn    = {1940-5901}
+}
+
+@article{Rettkowski2025,
+  author  = {Rettkowski, Jasmin and Romero-Mulero, Mari Carmen and Singh, Indranil and
+             Wadle, Carolin and Wrobel, Jan and Chiang, Diana and Hoppe, Natalie and
+             Mess, Julian and Sch{\"o}nberger, Katharina and Lalioti, Maria-Eleni and
+             J{\"a}cklein, Karin and SilvaRego, Beatriz and B{\"u}hler, Timon and
+             Karabacz, No{\'e}mie and Egg, Mirijam and Demollin, Helen and
+             Obier, Nadine and Zhang, Yu Wei and J{\"u}licher, Claus and
+             Hetkamp, Anne and Czerny, Martin and Jones, Michael-Jason and
+             Seung, Hana and Jain, Ritika and von zur M{\"u}hlen, Constantin and
+             Maier, Alexander and Lother, Achim and Hilgendorf, Ingo and
+             van Galen, Peter and Kreso, Antonia and Westermann, Dirk and
+             Rodriguez-Fraticelli, Alejo E. and Heidt, Timo and
+             Cabezas-Wallscheid, Nina},
+  title   = {Modulation of bone marrow haematopoietic stem cell activity as a therapeutic
+             strategy after myocardial infarction: a preclinical study},
+  journal = {Nature Cell Biology},
+  year    = {2025},
+  volume  = {27},
+  pages   = {591--604},
+  doi     = {10.1038/s41556-025-01639-4},
+  url     = {https://doi.org/10.1038/s41556-025-01639-4}
+}