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Slides to create heatmaps for. If multiple slides are given, the normalization of the attention / score maps' intensities will be performed across all slides.
Options
Description
-m MODEL_PATH, --model-path MODEL_PATH
MIL model used to generate attention / score maps.
-o OUTPUT_PATH, --output-path OUTPUT_PATH
Path to save results to.
-t TRUE_CLASS, --true-class TRUE_CLASS
Class to be rendered as "hot" in the heatmap.
--no-pool
Do not average pool features after feature extraction phase.
--cache-dir CACHE_DIR
Directory to cache extracted features etc. in.
Thresholds
Description
--mask-threshold THRESH
Brightness threshold for background removal.
--att-upper-threshold THRESH
Quantile to squash attention from during attention scaling (e.g. 0.99 will lead to the top 1% of attention scores to become 1)
--att-lower-threshold THRESH
Quantile to squash attention to during attention scaling (e.g. 0.01 will lead to the bottom 1% of attention scores to become 0)
--score-threshold THRESH
Quantile to consider in score scaling (e.g. 0.95 will discard the top / bottom 5% of score values as outliers)
Colors
Description
--att-cmap CMAP
Color map to use for the attention heatmap.
--score-cmap CMAP
Color map to use for the score heatmap.
Running in a Container
The heatmap script can be conveniently run in a podman container. To do so, use
the heatmaps-container.sh convenience script.