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medsam3-benchmark

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Image Segmentation
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medsam3
benchmark
box-prompt
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output
dict
la_003_left_atrium_z067
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 204, 177, 256, 270 ] }
{ "mask_format": "png_binary" }
la_004_left_atrium_z050
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 203, 203, 264, 302 ] }
{ "mask_format": "png_binary" }
la_005_left_atrium_z059
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 204, 174, 260, 276 ] }
{ "mask_format": "png_binary" }
la_007_left_atrium_z061
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 208, 187, 264, 275 ] }
{ "mask_format": "png_binary" }
la_009_left_atrium_z045
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 219, 212, 264, 308 ] }
{ "mask_format": "png_binary" }
la_010_left_atrium_z053
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 187, 203, 243, 288 ] }
{ "mask_format": "png_binary" }
la_011_left_atrium_z061
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 211, 188, 264, 291 ] }
{ "mask_format": "png_binary" }
la_014_left_atrium_z051
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 208, 187, 280, 278 ] }
{ "mask_format": "png_binary" }
la_016_left_atrium_z022
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 209, 200, 264, 284 ] }
{ "mask_format": "png_binary" }
la_017_left_atrium_z061
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "tight", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 228, 172, 280, 248 ] }
{ "mask_format": "png_binary" }
la_003_left_atrium_z067_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 196, 164, 253, 266 ] }
{ "mask_format": "png_binary" }
la_003_left_atrium_z067_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 209, 163, 272, 275 ] }
{ "mask_format": "png_binary" }
la_004_left_atrium_z050_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 198, 197, 266, 305 ] }
{ "mask_format": "png_binary" }
la_004_left_atrium_z050_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 188, 204, 262, 322 ] }
{ "mask_format": "png_binary" }
la_005_left_atrium_z059_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 196, 162, 257, 275 ] }
{ "mask_format": "png_binary" }
la_005_left_atrium_z059_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 204, 164, 271, 287 ] }
{ "mask_format": "png_binary" }
la_007_left_atrium_z061_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 198, 174, 259, 271 ] }
{ "mask_format": "png_binary" }
la_007_left_atrium_z061_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 192, 172, 259, 277 ] }
{ "mask_format": "png_binary" }
la_009_left_atrium_z045_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 215, 215, 265, 320 ] }
{ "mask_format": "png_binary" }
la_009_left_atrium_z045_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 221, 190, 275, 305 ] }
{ "mask_format": "png_binary" }
la_010_left_atrium_z053_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 182, 203, 243, 297 ] }
{ "mask_format": "png_binary" }
la_010_left_atrium_z053_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 176, 196, 243, 298 ] }
{ "mask_format": "png_binary" }
la_011_left_atrium_z061_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 208, 174, 266, 288 ] }
{ "mask_format": "png_binary" }
la_011_left_atrium_z061_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 217, 170, 281, 294 ] }
{ "mask_format": "png_binary" }
la_014_left_atrium_z051_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 209, 184, 288, 284 ] }
{ "mask_format": "png_binary" }
la_014_left_atrium_z051_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 196, 169, 283, 279 ] }
{ "mask_format": "png_binary" }
la_016_left_atrium_z022_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 204, 197, 264, 290 ] }
{ "mask_format": "png_binary" }
la_016_left_atrium_z022_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 194, 181, 260, 282 ] }
{ "mask_format": "png_binary" }
la_017_left_atrium_z061_jitter_expand10
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand10", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 229, 163, 286, 246 ] }
{ "mask_format": "png_binary" }
la_017_left_atrium_z061_jitter_expand20
{ "task": "segment", "target_label": "left_atrium", "prompt_type": "box", "text": "left atrium", "modality": "MR", "body_region": "cardiac", "box_variant": "jitter_expand20", "slice_note": "" }
{ "image_size": [ 512, 512 ], "box_xyxy": [ 221, 163, 284, 254 ] }
{ "mask_format": "png_binary" }

MedSAM3 Benchmark v2 (box-prompt evaluation)

Box-prompt segmentation benchmark. Each row is (instruction, input, output): a windowed full slice standardized to 512×512, a box_xyxy prompt (pixels, top-left origin), and a lossless binary PNG ground-truth mask.

How to consume (eval harness)

Read {split}/manifest.jsonl and load the {split}/images/*.png / {split}/masks/*.png files directly. These are lossless PNG — use them for Dice/IoU/HD95.

The Dataset Viewer thumbnails are a convenience preview; the datasets-server re-encodes thumbnails as JPEG. Do not score against the viewer thumbnails — always read the PNG files / parquet Image bytes, which are lossless.

Review fixes applied (v2)

  • Full slices, not crops — every slice is the full windowed image resized to 512×512; the box is the tight bbox of the target within the full slice (fixes inflated, non-comparable Dice).
  • Lossless PNG masks — masks are binary PNG (png_binary), never JPEG.
  • Jittered box variants — each sample includes tight, jitter_expand10 (+10%, ±8px) and jitter_expand20 (+20%, ±12px) box variants (see instruction.box_variant).

Splits

Split Source Modality Region Targets License Notes
totalsegmentator YongchengYAO/TotalSegmentator-CT-Lite CT Abdomen liver, spleen, kidneys CC BY 4.0 training-safe
m3d_seg GoodBaiBai88/M3D-Seg (KiPA22 / 0005) CT Abdomen kidney, kidney tumor research eval-only
msd MSD Task02 Heart MR Cardiac left atrium CC BY-SA 4.0 training-safe
busi_ultrasound huangjin520/busi-whu-seg US Breast breast tumor research eval-only
cads CADS VISCERAL GC CT Abdomen liver, spleen, pancreas, kidneys CC BY-NC-SA eval-only
hippocampus MSD Task04 Hippocampus MR Neuro hippocampus ant/post CC BY-SA 4.0 ROI crop — easy case
prostate MSD Task05 Prostate MR Pelvis prostate zones CC BY-SA 4.0 training-safe

Caveats

  • hippocampus uses MSD Task04's pre-cropped ROI volumes (~35×51) upscaled to 512×512 — intrinsically an easy case, not comparable to full-slice CT/MR splits. Labeled in instruction.slice_note.
  • Licensing — eval is fine for all splits. Training deployable weights: TotalSegmentator (CC BY 4.0) and MSD splits (CC BY-SA) only. cads (CC BY-NC-SA), m3d_seg/KiPA22 and busi_ultrasound are eval-only.
  • 2D only for v0; 3D volume-propagation is a planned follow-up.

Windowing (confirm matches production rendering)

Modality Window
CT WL 40 / WW 400
MR per-slice min–max
US native min–max
Downloads last month
140
Number of rows:
465
Total file size:
57 MB