| { |
| "model": "setup_53_2d", |
| "task": "mito_affinities", |
| "architecture": "Unet3dIso (2D-collapsed)", |
| "checkpoint": "student_60000", |
| "params": 1927907, |
| "channels": [ |
| "mito_aff_z", |
| "mito_aff_y", |
| "mito_aff_x" |
| ], |
| "input_voxel_size_nm": [ |
| 16, |
| 16, |
| 16 |
| ], |
| "output_voxel_size_nm": [ |
| 16, |
| 16, |
| 16 |
| ], |
| "output": "raw logits (apply sigmoid / threshold at 0)", |
| "input_norm": [ |
| { |
| "name": "MinMaxNormalizer", |
| "min_value": 0, |
| "max_value": 255 |
| }, |
| { |
| "name": "LambdaNormalizer", |
| "expression": "2*x-1" |
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| "io": "input 'input' float32 [1,1,1,y,x] (one z-slice); output 'output' float32 [1,C,1,y',x']", |
| "kind": "2D slice student distilled from the 3D model (train_2d_distill.py)", |
| "step": 60000, |
| "distilled_from": "setup_53", |
| "distilled_from_repo": "cellmap/mito-aff-unetiso-setup-53", |
| "variants": [ |
| { |
| "model": "setup_53_2d", |
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| 1, |
| 300, |
| 300 |
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| "file": "setup_53_mito_affinities_16nm_2d_in300_fp32.onnx", |
| "file_mb": 7.75, |
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| "flip_frac": 0.0 |
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| { |
| "model": "setup_53_2d", |
| "variant": "fp16", |
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| 300, |
| 300 |
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| 212, |
| 212 |
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| "file": "setup_53_mito_affinities_16nm_2d_in300_fp16.onnx", |
| "file_mb": 3.9, |
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| { |
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| 556, |
| 556 |
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| 468 |
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| "file": "setup_53_mito_affinities_16nm_2d_in556_fp32.onnx", |
| "file_mb": 7.75, |
| "max_abs": 2.09808349609375e-05, |
| "flip_frac": 0.0 |
| }, |
| { |
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| 556, |
| 556 |
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| 468 |
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| "file": "setup_53_mito_affinities_16nm_2d_in556_fp16.onnx", |
| "file_mb": 3.9, |
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| "flip_frac": 3.652567755131858e-05 |
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| { |
| "model": "setup_53_2d", |
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| 1068, |
| 1068 |
| ], |
| "output_size": [ |
| 1, |
| 980, |
| 980 |
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| "file": "setup_53_mito_affinities_16nm_2d_in1068_fp32.onnx", |
| "file_mb": 7.75, |
| "max_abs": 2.574920654296875e-05, |
| "flip_frac": 0.0 |
| }, |
| { |
| "model": "setup_53_2d", |
| "variant": "fp16", |
| "input_size": [ |
| 1, |
| 1068, |
| 1068 |
| ], |
| "output_size": [ |
| 1, |
| 980, |
| 980 |
| ], |
| "file": "setup_53_mito_affinities_16nm_2d_in1068_fp16.onnx", |
| "file_mb": 3.9, |
| "max_abs": 0.10926437377929688, |
| "flip_frac": 4.859086491739553e-05 |
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| ], |
| "val_f1": { |
| "metric": "affinity F1 (mean of 3 channels), 6 GT val crops, centered 200^3, threshold logit>0", |
| "student": { |
| "crop495": 0.8164, |
| "crop496": 0.796, |
| "crop1017": 0.9015, |
| "crop528": 0.9217, |
| "crop1091": 0.9166, |
| "crop1081": 0.9481 |
| }, |
| "student_mean": 0.8834, |
| "teacher_3d": { |
| "crop495": 0.955, |
| "crop496": 0.928, |
| "crop1017": 0.966, |
| "crop528": 0.9746, |
| "crop1091": 0.9517, |
| "crop1081": 0.9456 |
| }, |
| "teacher_3d_mean": 0.9535 |
| }, |
| "torch_version": "2.9.1", |
| "exporter": "torch.onnx.export (TorchScript, dynamo=False)", |
| "opset": 18, |
| "finetune": { |
| "head": { |
| "final_layer": "final_conv.c", |
| "onnx_node": "/final_conv/c/Conv", |
| "features": "/final_conv/Gather_output_0", |
| "weight": "final_conv.c.weight", |
| "bias": "final_conv.c.bias", |
| "in_channels": 32, |
| "out_channels": 3, |
| "activation": "none (logits)", |
| "files": [ |
| "setup_53_mito_affinities_16nm_2d_in1068_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in1068_fp32.onnx", |
| "setup_53_mito_affinities_16nm_2d_in300_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in300_fp32.onnx", |
| "setup_53_mito_affinities_16nm_2d_in556_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in556_fp32.onnx" |
| ], |
| "initializers": "finetune/initializers.json", |
| "loss": "masked BCE on logits", |
| "note": "train the final 1x1 conv on frozen features" |
| }, |
| "full": { |
| "library": "tfjs", |
| "files": [ |
| "finetune/train_graph.json", |
| "finetune/cellmap_tfjs_train.js" |
| ], |
| "weight_map": "identity", |
| "initializers": "finetune/initializers.json", |
| "write_back": [ |
| "setup_53_mito_affinities_16nm_2d_in1068_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in1068_fp32.onnx", |
| "setup_53_mito_affinities_16nm_2d_in300_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in300_fp32.onnx", |
| "setup_53_mito_affinities_16nm_2d_in556_fp16.onnx", |
| "setup_53_mito_affinities_16nm_2d_in556_fp32.onnx" |
| ], |
| "frozen": [ |
| "encoder0.bn1.running_mean", |
| "encoder0.bn1.running_var", |
| "encoder0.bn2.running_mean", |
| "encoder0.bn2.running_var", |
| "encoder1.bn1.running_mean", |
| "encoder1.bn1.running_var", |
| "encoder1.bn2.running_mean", |
| "encoder1.bn2.running_var", |
| "encoder2.bn1.running_mean", |
| "encoder2.bn1.running_var", |
| "encoder2.bn2.running_mean", |
| "encoder2.bn2.running_var", |
| "bottleneck.bn1.running_mean", |
| "bottleneck.bn1.running_var", |
| "bottleneck.bn2.running_mean", |
| "bottleneck.bn2.running_var", |
| "decoder2.bn1.running_mean", |
| "decoder2.bn1.running_var", |
| "decoder2.bn2.running_mean", |
| "decoder2.bn2.running_var", |
| "decoder1.bn1.running_mean", |
| "decoder1.bn1.running_var", |
| "decoder1.bn2.running_mean", |
| "decoder1.bn2.running_var", |
| "decoder0.bn1.running_mean", |
| "decoder0.bn1.running_var", |
| "decoder0.bn2.running_mean", |
| "decoder0.bn2.running_var" |
| ], |
| "note": "params named as the ONNX initializers; BatchNorm running stats frozen", |
| "spike": { |
| "setup": "TF.js 4.22.0 WebGPU backend, Chrome 154 on macOS, Apple GPU (metal-3, unified memory); batch 1, fp32, masked BCE on logits, Adam lr 1e-4; graph = finetune/train_graph.json, weights read from the served fp32 .onnx; median of 8 steps after 2 warm-up; peak = tf.profile peakBytes above baseline (tracked tensors; the WebGPU buffer pool holds more)", |
| "date": "2026-10-17", |
| "params": 1927907, |
| "full": { |
| "300": { |
| "step_ms": 308, |
| "peak_mb": 980 |
| }, |
| "556": { |
| "step_ms": 1189, |
| "peak_mb": 3897 |
| } |
| }, |
| "head_through_full_graph": { |
| "300": { |
| "step_ms": 31 |
| }, |
| "556": { |
| "step_ms": 133 |
| } |
| }, |
| "forward_ms": { |
| "300": 11, |
| "556": 41 |
| }, |
| "tfjs_webgpu_vs_ort_webgpu_556": { |
| "max_abs": 1.81e-05, |
| "flips": 0 |
| }, |
| "note": "2026-10-17 rerun of finetune_spike.html unchanged: peak_mb corrected (the 2026-10-16 values, 320/1307 MB for setup_53_2d, were not reproducible; this rerun matches an independent RTX 2080 Ti run: 980/3897 MB). Peak counts tracked tensors only, the WebGPU buffer pool holds more." |
| } |
| } |
| }, |
| "source_repo": "cellmap/mito-aff-unetiso-setup-53-2d" |
| } |
