Learning and documenting pathology informatics Designing responsible histopathology workflows
I am Dr. Fernando Soto, a physician and computer science graduate preparing for anatomical pathology residency. Histopath.ai is my public notebook: a living study path, annotated case library, and running project log for the pathology informatics work I build along the way. My current focus is whole-slide imaging pipelines, AI validation, and report-style pathology writing.
- Training
- MD and Computer Science graduate
- Focus
- Pathology informatics, WSI pipelines, AI validation and QA
- Current projects
- Breast carcinoma WSI pipeline, DCP 601–602 notes, ML metrics notebook
- Goal
- Anatomical pathology residency with emphasis on pathology informatics
About
Who I am, why I built histopath.ai, and how to reach me.
Visit sectionCase Library
Educational case reports emphasising terminology, diagnostic reasoning, and QA follow-ups.
Visit sectionReference guide
Quick-reference docs for datasets, tissue guides, and mathematics refreshers.
Visit sectionProjects
Deep learning, automation, and data projects that bridge histology practice with engineering.
Visit sectionReference docs
Latest reference documents
Freshly updated articles from docs.histopath.ai. New pages will appear here automatically as they’re added to the reference guide.
3/4/2026
Step 3 – Preprocessing & QC (The Grossing Room)
OpenCV, NumPy, and Libvips blocks for tissue masking, mask cleaning, blur detection, and tiling before modeling.
3/4/2026
Preprocessing & QC
Trim, clean, and standardize slides before analysis—crop, tile, filter, and normalize.
3/4/2026
Websites Quick Reference
Curated external sites for deepening histology fundamentals and sourcing open histopathology datasets.
3/4/2026
Initial System Setup
All-in-one Linux bootstrap for DCP work (Ubuntu/Debian and Arch-based distros) to install Docker, VS Code, Git, and Miniconda.
3/4/2026
Step 2 – Slides & Viewing (The Digital Microscope)
OpenSlide, Pillow, and Matplotlib blocks to read WSIs, view thumbnails and regions, and sanity-check patch grids from cohort CSVs.
3/4/2026
Slides & Viewing
Open, zoom, and compare whole‑slide images using clinician‑friendly desktop and web viewers.
Latest cases
Practice cases with report-style write-ups
Every case captures diagnostic language, QA follow-ups, and the questions I bring to attending pathologists.
Featured project
Breast Carcinoma WSI Pipeline
Reproducible workflow for tiling, training, and reporting attention-based slide classifiers on invasive breast carcinoma.
- Standardised patch extraction and stain normalisation using reproducible configs.
- Slide-level attention pooling with integrated attribution overlays for case review.
- Validation dashboards aligned with CAP/CLIA quality metrics and internal QA checks.
Notebook updates
What I’m reading and shipping
Short reflections on papers, conferences, and project milestones that influence the study path. Updated as I learn, usually monthly.
View notebook archive →Let’s compare notes
I welcome feedback, mentorship, and collaboration opportunities, especially from teams building pathology informatics infrastructure or evaluating AI tools. Reach out if you spot gaps, want to share material, or a partner on validation work.
- fsoto@histopath.ai
- GitHub
- github.com/drsoma
- ORCID
- 0009-0007-5857-3476