Evaluation
- ID
- 68ef86b4-baad-4ac1-8083-a7d9af9fb82f
- Submission ID
- 1b98b8bc-b214-45a1-971b-df7255448b7a
- Method ID
- dc854b14-ba0a-43df-af86-bc99177f9066
- Status
-
Succeeded
- User
-
danieleek
- Challenge
-
PUMA
- Phase
-
Track 2: Preliminary test phase
- Algorithm
-
Track 2: Baseline (HoVer-NeXt + nnU-net)
(Image Version b06f2364-214f-4da3-b7e5-9b1587723151
)
- Submission created
- Sept. 30, 2024, 2:03 p.m.
- Result created
- Oct. 1, 2024, 6:50 p.m.
- Position on leaderboard
-
69
- Comment:
Metrics
{
"results": [
{
"filename": "preliminary_test_set_metastatic_roi_005.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.20420048161067544
},
"micro": {
"recall": 0.5350877192982456,
"f1_score": 0.5083333333333334,
"precision": 0.48412698412698413
},
"nuclei_tumor": {
"FN": 13,
"FP": 116,
"TP": 74,
"recall": 0.8505747126436781,
"f1_score": 0.5342960288808664,
"precision": 0.3894736842105263
},
"nuclei_stroma": {
"FN": 6,
"FP": 19,
"TP": 2,
"recall": 0.25,
"f1_score": 0.13793103448275862,
"precision": 0.09523809523809523
},
"nuclei_apoptosis": {
"FN": 2,
"FP": 4,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_histiocyte": {
"FN": 103,
"FP": 5,
"TP": 13,
"recall": 0.11206896551724138,
"f1_score": 0.19402985074626866,
"precision": 0.7222222222222222
},
"nuclei_lymphocyte": {
"FN": 26,
"FP": 31,
"TP": 94,
"recall": 0.7833333333333333,
"f1_score": 0.7673469387755101,
"precision": 0.752
},
"nuclei_endothelium": {
"FN": 0,
"FP": 13,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_melanophage": {
"FN": 6,
"FP": 6,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_plasma_cell": {
"FN": 3,
"FP": 1,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.7214900196839318,
"tissue_tumor": 0.8826242338631402,
"tissue_stroma": 0.7248258642639158,
"tissue_necrosis": 2.926029961690651e-10,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 1.0
}
},
{
"filename": "preliminary_test_set_primary_roi_002.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.27342889647914115
},
"micro": {
"recall": 0.6581081081081082,
"f1_score": 0.6982078853046596,
"precision": 0.7435114503816794
},
"nuclei_tumor": {
"FN": 43,
"FP": 108,
"TP": 200,
"recall": 0.823045267489712,
"f1_score": 0.7259528130671506,
"precision": 0.6493506493506493
},
"nuclei_stroma": {
"FN": 10,
"FP": 6,
"TP": 2,
"recall": 0.16666666666666666,
"f1_score": 0.2,
"precision": 0.25
},
"nuclei_apoptosis": {
"FN": 4,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_histiocyte": {
"FN": 42,
"FP": 3,
"TP": 1,
"recall": 0.023255813953488372,
"f1_score": 0.0425531914893617,
"precision": 0.25
},
"nuclei_lymphocyte": {
"FN": 154,
"FP": 29,
"TP": 282,
"recall": 0.6467889908256881,
"f1_score": 0.7550200803212851,
"precision": 0.9067524115755627
},
"nuclei_endothelium": {
"FN": 0,
"FP": 17,
"TP": 2,
"recall": 1.0,
"f1_score": 0.1904761904761905,
"precision": 0.10526315789473684
},
"nuclei_plasma_cell": {
"FN": 0,
"FP": 5,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.5683894686364102,
"tissue_tumor": 0.9279740245816764,
"tissue_stroma": 0.9139733082556122,
"tissue_necrosis": 8.264462741616011e-09,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 2.0802995588094456e-09
}
},
{
"filename": "preliminary_test_set_metastatic_roi_003.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.18930094142558732
},
"micro": {
"recall": 0.7952218430034129,
"f1_score": 0.7898305084745763,
"precision": 0.7845117845117845
},
"nuclei_tumor": {
"FN": 66,
"FP": 79,
"TP": 457,
"recall": 0.8738049713193117,
"f1_score": 0.8630783758262512,
"precision": 0.8526119402985075
},
"nuclei_stroma": {
"FN": 41,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_apoptosis": {
"FN": 0,
"FP": 1,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_lymphocyte": {
"FN": 13,
"FP": 35,
"TP": 9,
"recall": 0.4090909090909091,
"f1_score": 0.27272727272727276,
"precision": 0.20454545454545456
},
"nuclei_endothelium": {
"FN": 0,
"FP": 8,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_plasma_cell": {
"FN": 0,
"FP": 5,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.5989769061505983,
"tissue_tumor": 0.9948845293302716,
"tissue_stroma": 9.095043193183227e-10,
"tissue_necrosis": 5.132152935523658e-10,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 1.0
}
},
{
"filename": "preliminary_test_set_metastatic_roi_004.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.3570597819547399
},
"micro": {
"recall": 0.6552462526766595,
"f1_score": 0.6289825282631037,
"precision": 0.6047430830039525
},
"nuclei_tumor": {
"FN": 34,
"FP": 24,
"TP": 83,
"recall": 0.7094017094017094,
"f1_score": 0.7410714285714285,
"precision": 0.7757009345794392
},
"nuclei_stroma": {
"FN": 13,
"FP": 12,
"TP": 13,
"recall": 0.5,
"f1_score": 0.5098039215686274,
"precision": 0.52
},
"nuclei_apoptosis": {
"FN": 6,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_histiocyte": {
"FN": 8,
"FP": 27,
"TP": 10,
"recall": 0.5555555555555556,
"f1_score": 0.36363636363636365,
"precision": 0.2702702702702703
},
"nuclei_lymphocyte": {
"FN": 26,
"FP": 116,
"TP": 193,
"recall": 0.8812785388127854,
"f1_score": 0.7310606060606061,
"precision": 0.6245954692556634
},
"nuclei_endothelium": {
"FN": 0,
"FP": 18,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_plasma_cell": {
"FN": 74,
"FP": 3,
"TP": 7,
"recall": 0.08641975308641975,
"f1_score": 0.15384615384615385,
"precision": 0.7
}
},
"tissue_metrics": {
"average_dice": 0.778100545916816,
"tissue_tumor": 0.945924261874708,
"tissue_stroma": 0.9445784200903268,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 4.7619045351474034e-08
}
},
{
"filename": "preliminary_test_set_primary_roi_003.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.43357123538294917
},
"micro": {
"recall": 0.651394422310757,
"f1_score": 0.6456071076011847,
"precision": 0.639921722113503
},
"nuclei_tumor": {
"FN": 27,
"FP": 66,
"TP": 122,
"recall": 0.8187919463087249,
"f1_score": 0.7240356083086055,
"precision": 0.648936170212766
},
"nuclei_stroma": {
"FN": 12,
"FP": 11,
"TP": 2,
"recall": 0.14285714285714285,
"f1_score": 0.14814814814814817,
"precision": 0.15384615384615385
},
"nuclei_apoptosis": {
"FN": 2,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_histiocyte": {
"FN": 69,
"FP": 55,
"TP": 52,
"recall": 0.4297520661157025,
"f1_score": 0.456140350877193,
"precision": 0.48598130841121495
},
"nuclei_lymphocyte": {
"FN": 61,
"FP": 25,
"TP": 143,
"recall": 0.7009803921568627,
"f1_score": 0.7688172043010754,
"precision": 0.8511904761904762
},
"nuclei_endothelium": {
"FN": 0,
"FP": 24,
"TP": 3,
"recall": 1.0,
"f1_score": 0.19999999999999998,
"precision": 0.1111111111111111
},
"nuclei_melanophage": {
"FN": 2,
"FP": 2,
"TP": 3,
"recall": 0.6,
"f1_score": 0.6,
"precision": 0.6
},
"nuclei_plasma_cell": {
"FN": 2,
"FP": 1,
"TP": 2,
"recall": 0.5,
"f1_score": 0.5714285714285715,
"precision": 0.6666666666666666
}
},
"tissue_metrics": {
"average_dice": 0.858081947616624,
"tissue_tumor": 0.7246983452677128,
"tissue_stroma": 0.7173004055166462,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 0.8484109872987616
}
},
{
"filename": "preliminary_test_set_primary_roi_004.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.3744947004726112
},
"micro": {
"recall": 0.6216216216216216,
"f1_score": 0.6262376237623762,
"precision": 0.6309226932668329
},
"nuclei_tumor": {
"FN": 53,
"FP": 51,
"TP": 65,
"recall": 0.5508474576271186,
"f1_score": 0.5555555555555556,
"precision": 0.5603448275862069
},
"nuclei_stroma": {
"FN": 8,
"FP": 23,
"TP": 11,
"recall": 0.5789473684210527,
"f1_score": 0.4150943396226416,
"precision": 0.3235294117647059
},
"nuclei_epithelium": {
"FN": 36,
"FP": 0,
"TP": 6,
"recall": 0.14285714285714285,
"f1_score": 0.25,
"precision": 1.0
},
"nuclei_histiocyte": {
"FN": 34,
"FP": 36,
"TP": 25,
"recall": 0.423728813559322,
"f1_score": 0.41666666666666663,
"precision": 0.4098360655737705
},
"nuclei_lymphocyte": {
"FN": 18,
"FP": 20,
"TP": 145,
"recall": 0.8895705521472392,
"f1_score": 0.8841463414634148,
"precision": 0.8787878787878788
},
"nuclei_endothelium": {
"FN": 1,
"FP": 17,
"TP": 1,
"recall": 0.5,
"f1_score": 0.09999999999999999,
"precision": 0.05555555555555555
},
"nuclei_melanophage": {
"FN": 4,
"FP": 1,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.8863063756463049,
"tissue_tumor": 0.7203122220934697,
"tissue_stroma": 0.8581860379560537,
"tissue_necrosis": 1.0,
"tissue_epidermis": 0.8530336181820015,
"tissue_blood_vessel": 1.0
}
},
{
"filename": "preliminary_test_set_metastatic_roi_002.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.24405188631806987
},
"micro": {
"recall": 0.7142857142857143,
"f1_score": 0.7352941176470589,
"precision": 0.7575757575757576
},
"nuclei_tumor": {
"FN": 45,
"FP": 53,
"TP": 170,
"recall": 0.7906976744186046,
"f1_score": 0.776255707762557,
"precision": 0.7623318385650224
},
"nuclei_stroma": {
"FN": 10,
"FP": 2,
"TP": 1,
"recall": 0.09090909090909091,
"f1_score": 0.14285714285714288,
"precision": 0.3333333333333333
},
"nuclei_apoptosis": {
"FN": 1,
"FP": 2,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_histiocyte": {
"FN": 16,
"FP": 13,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_lymphocyte": {
"FN": 108,
"FP": 41,
"TP": 279,
"recall": 0.7209302325581395,
"f1_score": 0.7892503536067892,
"precision": 0.871875
},
"nuclei_endothelium": {
"FN": 0,
"FP": 26,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_plasma_cell": {
"FN": 0,
"FP": 7,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.9656841244207037,
"tissue_tumor": 0.9514332195132319,
"tissue_stroma": 0.8769874025902863,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 1.0
}
},
{
"filename": "preliminary_test_set_primary_roi_001.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.3743575430066327
},
"micro": {
"recall": 0.725,
"f1_score": 0.7250000000000001,
"precision": 0.725
},
"nuclei_tumor": {
"FN": 102,
"FP": 28,
"TP": 219,
"recall": 0.6822429906542056,
"f1_score": 0.7711267605633804,
"precision": 0.8866396761133604
},
"nuclei_stroma": {
"FN": 0,
"FP": 7,
"TP": 3,
"recall": 1.0,
"f1_score": 0.4615384615384615,
"precision": 0.3
},
"nuclei_apoptosis": {
"FN": 0,
"FP": 0,
"TP": 1,
"recall": 1.0,
"f1_score": 1.0,
"precision": 1.0
},
"nuclei_histiocyte": {
"FN": 0,
"FP": 27,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_lymphocyte": {
"FN": 30,
"FP": 48,
"TP": 125,
"recall": 0.8064516129032258,
"f1_score": 0.7621951219512195,
"precision": 0.7225433526011561
},
"nuclei_endothelium": {
"FN": 0,
"FP": 18,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_melanophage": {
"FN": 0,
"FP": 2,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_plasma_cell": {
"FN": 0,
"FP": 2,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 0.5987529743472201,
"tissue_tumor": 0.9937648651229549,
"tissue_stroma": 8.890469408881163e-10,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 5.724098421728115e-09
}
},
{
"filename": "preliminary_test_set_metastatic_roi_001.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.18725420516465294
},
"micro": {
"recall": 0.5785953177257525,
"f1_score": 0.5626016260162601,
"precision": 0.5474683544303798
},
"nuclei_tumor": {
"FN": 89,
"FP": 26,
"TP": 110,
"recall": 0.5527638190954773,
"f1_score": 0.6567164179104478,
"precision": 0.8088235294117647
},
"nuclei_stroma": {
"FN": 0,
"FP": 31,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_apoptosis": {
"FN": 0,
"FP": 6,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_histiocyte": {
"FN": 0,
"FP": 7,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_lymphocyte": {
"FN": 1,
"FP": 23,
"TP": 9,
"recall": 0.9,
"f1_score": 0.4285714285714286,
"precision": 0.28125
},
"nuclei_neutrophil": {
"FN": 0,
"FP": 2,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_endothelium": {
"FN": 0,
"FP": 4,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
},
"nuclei_melanophage": {
"FN": 36,
"FP": 36,
"TP": 54,
"recall": 0.6,
"f1_score": 0.6,
"precision": 0.6
},
"nuclei_plasma_cell": {
"FN": 0,
"FP": 8,
"TP": 0,
"recall": 0,
"f1_score": 0,
"precision": 0.0
}
},
"tissue_metrics": {
"average_dice": 1.0,
"tissue_tumor": 1.0,
"tissue_stroma": 1.0,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 1.0
}
},
{
"filename": "preliminary_test_set_primary_roi_005.tif",
"nuclei_metrics": {
"macro": {
"f1_score": 0.38449069885704623
},
"micro": {
"recall": 0.7471526195899773,
"f1_score": 0.7354260089686099,
"precision": 0.7240618101545254
},
"nuclei_tumor": {
"FN": 46,
"FP": 31,
"TP": 228,
"recall": 0.8321167883211679,
"f1_score": 0.8555347091932457,
"precision": 0.8803088803088803
},
"nuclei_stroma": {
"FN": 3,
"FP": 11,
"TP": 2,
"recall": 0.4,
"f1_score": 0.2222222222222222,
"precision": 0.15384615384615385
},
"nuclei_apoptosis": {
"FN": 6,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_histiocyte": {
"FN": 30,
"FP": 22,
"TP": 21,
"recall": 0.4117647058823529,
"f1_score": 0.44680851063829785,
"precision": 0.4883720930232558
},
"nuclei_lymphocyte": {
"FN": 7,
"FP": 32,
"TP": 63,
"recall": 0.9,
"f1_score": 0.7636363636363636,
"precision": 0.6631578947368421
},
"nuclei_neutrophil": {
"FN": 2,
"FP": 0,
"TP": 0,
"recall": 0.0,
"f1_score": 0,
"precision": 0
},
"nuclei_endothelium": {
"FN": 6,
"FP": 27,
"TP": 9,
"recall": 0.6,
"f1_score": 0.35294117647058826,
"precision": 0.25
},
"nuclei_melanophage": {
"FN": 11,
"FP": 2,
"TP": 5,
"recall": 0.3125,
"f1_score": 0.43478260869565216,
"precision": 0.7142857142857143
}
},
"tissue_metrics": {
"average_dice": 0.8707800052658179,
"tissue_tumor": 0.9442140483797589,
"tissue_stroma": 0.9082347289800585,
"tissue_necrosis": 1.0,
"tissue_epidermis": 1.0,
"tissue_blood_vessel": 0.5014512489692725
}
}
],
"aggregates": {
"f1_nuclei": {
"nuclei_tumor": 0.7203623405639489,
"nuclei_stroma": 0.22375952704400026,
"nuclei_apoptosis": 0.1,
"nuclei_epithelium": 0.025,
"nuclei_histiocyte": 0.19198349340541515,
"nuclei_lymphocyte": 0.6922771711414966,
"nuclei_neutrophil": 0.0,
"nuclei_endothelium": 0.08434173669467787,
"nuclei_melanophage": 0.1634782608695652,
"nuclei_plasma_cell": 0.07252747252747253
},
"dice_tissue": {
"average_dice": 0.7846562367684426,
"tissue_tumor": 0.9085829750026925,
"tissue_stroma": 0.6944086169451451,
"tissue_necrosis": 0.7000000009070281,
"tissue_epidermis": 0.9853033618182001,
"tissue_blood_vessel": 0.6349862291691477
},
"macro_f1_nuclei": 0.22737300022465762,
"micro_dice_tissue": {
"tissue_tumor": 0.9336662271538972,
"tissue_stroma": 0.8491917439728844,
"tissue_necrosis": 0.0,
"tissue_epidermis": 0.8530336181820015,
"average_micro_dice": 0.6288325593585905,
"tissue_blood_vessel": 0.5082712074841697
}
}
}