Pathogene

PATHOGENE —

Sample QC

Unreviewed

Annotation Key

Tumor

Stroma

Other / In-situ

Lymphocyte

Draw Annotation

CosMx Manual Align

Rotation: 0°

Scale: 1.00x

AI Lymphocyte Threshold

Score Distribution

Threshold 0.10

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Displayed

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Of Total

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Hidden

No data loaded

🔬

No slides registered yet.

Ready

Annotations: 0

Independent panels

PATHOGENE Registration

Register New Slide

Select local file paths, preview the slide, then start the pipeline.

✓

🔬

H&E Slide

Click to browse
.svs / .tif / .tiff

✓

🧬

CosMx Image

Click to browse
.png

Optional

Processing

0 / 0

Registration Preview

Does the CosMx overlay align well with the H&E? Use the opacity slider to check.

CosMx opacity 50%

PATHOGENE Rigid Body Step 2 Anchor Placement Scroll: zoom | Drag: pan | Click: place anchor

H&E SLIDE Click to place anchor

Loading H&E...

100%

COSMX IMAGE Click H&E first

Loading CosMx...

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