> For the complete documentation index, see [llms.txt](https://www.parapathology.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://www.parapathology.com/computational-digital-and-mathematical-pathology/image-analysis.md).

# Image Analysis

[Training deep AI pipelines with Biodock](https://www.youtube.com/watch?v=yUNyonBgBIs\&ab_channel=MichaelLee)

{% embed url="<https://www.youtube.com/watch?v=yUNyonBgBIs&ab_channel=MichaelLee>" %}

{% embed url="<https://www.youtube.com/watch?v=9fEDSOUbGFA&t=1955s&ab_channel=TIAWarwick>" %}

## Bioimage Analysis 2020

#### [01a Introduction to Bio-Image Analysis](https://www.youtube.com/watch?v=e-2DbkUwKk4)

{% embed url="<https://www.youtube.com/watch?v=e-2DbkUwKk4>" %}

#### [01b Introduction to Bio-Image Analysis with Fiji](https://www.youtube.com/watch?v=Akedfyp5AxY)

{% embed url="<https://www.youtube.com/watch?v=Akedfyp5AxY>" %}

#### [lecture\_applied\_bioimage\_analysis\_2020](https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020)

{% embed url="<https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis_2020>" %}

## Image Analysis

* Grand Challenges in Biomedical Image Analysis: [grand-challenge.org](https://grand-challenge.org/)
* Fiji: [fiji.sc](https://fiji.sc/)
* 3D Volumetric Pathology Triage: [TRICARE: Deep-learning triage of 3D pathology datasets](https://github.com/sbalci/ParaPathology/tree/master/computational-digital-and-mathematical-pathology/tricare-deep-learning-triage-3d-pathology.md) — 2.5D context-aware deep learning framework for triaging open-top light-sheet microscopy (OTLS) datasets in prostate and Barrett's esophagus biopsies (Gao et al., *Nature Biomedical Engineering* 2026).