---
title: Pathology troubleshooting
description: Fix empty tile sets, missing slide URLs, unsupported workflows, and slide-loading failures.
---

When a [pathology](/docs/pathology) run fails or returns fewer results than you expected, the cause is usually the slide reference, the quality filters, or the workflow you chose. This page covers the common failure modes and how to resolve them.

## "Missing required parameter 'slide_url'"

The job needs an S3 URI to the slide as its one required input.

- Upload the whole slide image to workspace storage first, then reference it by its `s3://…` URI.
- Confirm the URI is well-formed — the tool rejects paths that do not start with `s3://`.

## The tile set is empty or tiny

Tile extraction discards any tile that fails the tissue or blur filter, so a filter set too strict for your slide yields few or no tiles.

- Lower `tissue_threshold` (default 0.5) if much of the slide is faintly stained or sparse.
- Lower `blur_threshold` (default 100.0, Laplacian variance) if in-focus regions are being dropped as blurry.
- Check the magnification — tiling at `40x` over a small image can leave too little area per tile.

## "Unsupported workflow"

The processor runs `tile_extraction`, `tissue_detection`, and `feature_extraction`. If you request a workflow it cannot execute, it raises an unsupported-workflow error.

- Pick one of the three operational workflows for slide processing.
- For tissue-typing or cell-level tasks, start from tile extraction or feature extraction and analyze downstream.

## The slide will not open

The tool opens SVS, NDPI, and pyramidal TIFF via histolab/OpenSlide, falling back to PIL for standard images.

- Confirm the file is a supported format (SVS, TIFF, NDPI, PNG, JPG).
- Corrupt or truncated slide files fail to load — re-upload from the source.
- Standard PNG/JPG images work but do not carry pyramidal magnification metadata, so the `magnification` setting has no effect on them.

## The job runs a long time

Runs are asynchronous and can take **10–60 minutes**; very large slides process tile by tile with a heartbeat.

- Cap the workload with `max_tiles` (default 1000) to bound tile extraction.
- Ensure sufficient storage for intermediate tiles — large WSI files are processed in tiles.

## Feature extraction returns no features

- If tile extraction found no tiles, feature extraction has nothing to process — fix the tile filters first (see above).
- Confirm `save_features` is on so the `features.npy` artifact is uploaded.

## Guest access denied

Pathology analysis is an authenticated, professional-tier tool. If you hit a guest-access-denied response, sign in with an account that has access.

## Read next