# QuPath guide for H-DAB Cell Counting Docs ## About To follow this step-by-step Guide no previous knowledge of QuPath, Git Bash, or Python is needed. All you need to follow in this tutorial is **H-DAB stained, slide-scanned samples**. The installation of the programs/software needed and the explanation of how to navigate through them can all be found in this Gitbook. If you use this step by step guide, please cite the paper below: Nüesch, A., Ferri, M. P., & Le Maitre, C. L. (2025). Application and Validation of Semiautomatic Quantification of Immunohistochemically Stained Sections for Low Cellular Tissue Such as Intervertebral Disc Using QuPath. *JOR Spine*, *8*(1), e70054. ## General Information QuPath is an open-source software for bioimage analysis and is often used for digital pathology. Its user-friendly interface, built-in algorithms for tissue and cell detection, the ability for interactive machine learning, and the possibility for automated scripting provide a powerful tool for whole slide image analysis. This project aimed to create a script for semi-automatic cell counting in QuPath, particularly for tissues with high extracellular matrix-to-cell ratio, which produces reproducible immunopositivity rates, with high accuracy, and reduced time to evaluate the samples and is a non-black-box approach. We advise you to use the processMRXS Package tutorial for the conversion of the text result files from QuPath. If you do not want to use the code to convert the files and merge them, they can be manually opened in Excel and further analysed from there. > **License**: > > Bankhead, P. et al. **QuPath: Open source software for digital pathology image analysis**. *Scientific Reports* (2017).\ > ## Overview This guide is for the QuPath extension for H-DAB Cell counting and classification in tissue and has been specifically developed within the [Disc4all ITN](https://disc4all.upf.edu/) project. The docs will consist of two sections: {% content-ref url="/pages/QrfWGkWOCYrTJjFmuQ7H" %} [Simple Pipeline](/qupath-project/pipeline/simple-pipeline.md) {% endcontent-ref %} {% content-ref url="/pages/W1EkEFkE9CQyaoxjYwgV" %} [QuPath H-DAB Tutorial](/qupath-project/qupath-h-dab-docs/qupath-h-dab-tutorial.md) {% endcontent-ref %} {% content-ref url="/pages/eeUEmiUvdm5kzlIpAH5s" %} [Processing Package Tutorial](/qupath-project/result-analysis-docs/processing-package-tutorial.md) {% endcontent-ref %} ## Get Started We've put together some helpful guides, for you to get set up with our product quickly and easily, for expert or non-expert usage. {% content-ref url="/pages/qegIgQ8SXtw5thDUIbAp" %} [Getting Set Up](/qupath-project/fundamentals/getting-set-up.md) {% endcontent-ref %} {% content-ref url="/pages/SAvM5ruf5sNgSRgW5CHi" %} [QuPath Installation](/qupath-project/non-expert-docs/qupath-installation.md) {% endcontent-ref %} {% content-ref url="/pages/Z5pOkqTaPCubDdNWv2KP" %} [Git Bash Installation](/qupath-project/non-expert-docs/git-bash-installation.md) {% endcontent-ref %} {% content-ref url="/pages/4UwuBYLdNxlNuXdx53Op" %} [Python Installation & Packages](/qupath-project/non-expert-docs/python-installation-and-packages.md) {% endcontent-ref %} --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://disc4all-qupath.gitbook.io/qupath-project/qupath-guide-for-h-dab-cell-counting-docs.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.