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deeperfly-models

Keypoint Detection
pose-estimation
multi-view
drosophila
neuroscience
deeperfly
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Add 260927_mvt_dinov3b_384_octacam_fly38

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  1. 260927_mvt_dinov3b_384_octacam_fly38/README.md +29 -0
  2. 260927_mvt_dinov3b_384_octacam_fly38/SHA256SUMS +4 -0
  3. 260927_mvt_dinov3b_384_octacam_fly38/config.toml +94 -0
  4. 260927_mvt_dinov3b_384_octacam_fly38/fly38.toml +129 -0
  5. 260927_mvt_dinov3b_384_octacam_fly38/mvt_dinov3b_384_octacam_fly38.pth +3 -0
  6. 260927_mvt_dinov3b_384_octacam_fly38/report.json +154 -0
260927_mvt_dinov3b_384_octacam_fly38/README.md ADDED
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+ # `mvt_dinov3b_384_octacam_fly38` -- the octacam detector, round 11
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+
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+ A deeperfly 2 detector (`deeperfly-detector-1`, family `mvt`): a multiview transformer on a DINOv3 ViT-B/16 that predicts all 38 points of the `fly38` skeleton in every view of the octacam rig, computing the views of a frame together. It supersedes `260904_mvt_dinov3s_384_gray_fly38` on this rig.
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+
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+ Exported 2026-09-28 from `octacam/runs/mvt_dinov3/round11/r11_ship_s0`, trained 2026-09-27: round 8's recipe unchanged (warm-started from a pseudo-labeled ViT-B, lr 1e-4, 5,000 steps, a distillation stream on unlabeled frames), retrained on the labels of 2026-09-27.
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+
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+ | | |
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+ |---|---|
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+ | file | `mvt_dinov3b_384_octacam_fly38.pth`, 383,792,459 bytes |
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+ | sha256 | `6898ccc26d454d26792cc5a125053cc3ffe15c8295c0182eae33c4da6d921f19` |
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+ | skeleton | `fly38` -- `fly38.toml` beside this file |
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+ | backbone | `vit_base_patch16_dinov3.lvd1689m` (timm) |
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+ | input | 384x768 per view: a 2:1 window around the animal |
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+ | trained on | 56 octacam recordings, 4,488 items (`report.json`); no holdout |
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+ | recipe | `config.toml` beside this file |
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+
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+ ## What it scores
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+
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+ No held-out number of its own: a shipping model trains on every label. On the deeperfly repository's `examples/octacam/` clip (200 frames of `scape_260417_IN07B001_Fly4_006`), the example run config's bundle adjustment takes an orbit guess from 172 px to 1.9 px median reprojection, and the pictorial 3D then reprojects at 1.49 px median. That is agreement across the eight views, not an error against labels.
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+
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+ ## Using it
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+
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+ ```toml
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+ [pose2d]
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+ weights = ["/mnt/upramdya/data/TL/deeperfly-models/260927_mvt_dinov3b_384_octacam_fly38/mvt_dinov3b_384_octacam_fly38.pth"]
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+ candidates = 5 # the peaks [pose3d] method = "pictorial" chooses among
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+ ```
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+
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+ Copying this directory to the machine that runs it and naming the local path is the better habit. Verify a copy with `sha256sum -c SHA256SUMS`.
260927_mvt_dinov3b_384_octacam_fly38/SHA256SUMS ADDED
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+ af81f78994be135442be6cc47cb09ff98f450915c2619b5dc95705b94baaf54f ./config.toml
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+ 56f9a33ea5c286bda06e599602e7b7adaefb7ba29a74a2516548b7cbb7776e52 ./fly38.toml
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+ 6898ccc26d454d26792cc5a125053cc3ffe15c8295c0182eae33c4da6d921f19 ./mvt_dinov3b_384_octacam_fly38.pth
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+ fbfefcbaa0eeee661467eacf14277190472610dd17f7eaae3030259960d25f97 ./report.json
260927_mvt_dinov3b_384_octacam_fly38/config.toml ADDED
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+ # r11_ship_s0: round 11's corpus ship -- r8_ship_s0's recipe unchanged (warm DINOv3
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+ # ViT-B from `tier1/vitb_stage2_pseudo`, lr 1e-4, 5k-step cosine, fill 0.5, the
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+ # distillation stream from `tier1/c6_vitb_warm_5k`), retrained on the labels of
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+ # 2026-09-27 by the code of main 796ae43. round11/ sits at round8/'s depth, so every
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+ # relative path is the same; only `out` moves.
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+
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+ format_version = 3
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+
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+ [data]
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+ kind = "project"
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+ projects = ["../../../recordings/*"]
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+ cache = "../../../cache"
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+
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+ [data.crops]
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+ tightness = [0.75, 2.2] # per-sample 2:1 crop around the animal, log-uniform;
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+ jitter = 0.1 # < 1 leaves points outside on purpose
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+ eval_tightness = 1.25
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+ full_p = 0.1 # letterboxed whole frame (an inference without any crop)
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+
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+ [data.fill]
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+ weight = 0.5
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+ max_residual_px = 10.0
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+
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+ [model]
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+ input_hw = [384, 768]
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+ family = "mvt"
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+ backbone = "vit_base_patch16_dinov3.lvd1689m"
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+ pretrained = true
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+ attn_scopes = "llllllllglgl"
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+ margin = 64
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+ reach = 2
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+ drop_path = 0.0
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+ token_mask = 0.0
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+ token_pad = 2 # 32 px of the 64 px margin in the token grid (1.26x tokens)
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+ init_from = "/home/tlam/deeperfly-projects/octacam/runs/mvt_dinov3/tier1/vitb_stage2_pseudo/model.pth"
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+
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+ [augment]
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+ degrees = 12.0
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+ scale = [1.0, 1.0] # the crop sampler supplies scale and shift
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+ aspect = [0.85, 1.18]
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+ translate = [0.0, 0.0]
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+ flip_p = 0.5
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+ brightness = 0.3
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+ contrast = 0.3
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+ gamma = [0.7, 1.4]
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+ blur_sigma = [0.5, 1.5]
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+ noise_std = 0.03
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+ photometric_p = 0.5
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+
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+ [train]
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+ grad_checkpoint = true
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+ steps = 5000
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+ images_per_batch = 24
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+ grad_clip = 1.0
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+ amp = true
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+ ema_decay = 0.999
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+ view_drop_p = 0.3
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+ view_min = 1
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+ log_every = 100
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+ seed = 0
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+ out = "../../../runs/mvt_dinov3/round11/r11_ship_s0"
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+
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+ [train.optimizer]
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+ lr = 1e-4
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+ weight_decay = 0.05
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+ warmup_steps = 500
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+
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+ [train.loss]
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+ sigma = 2.0
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+ field_weight = 1.0
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+ coord_weight = 0.0
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+ tri_weight = 0.02
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+ tri_huber = 0.05
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+ tri_max_world = 0.5
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+
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+ [train.eval]
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+ every = 0
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+
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+ [compute]
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+ workers = 8
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+
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+ [unlabeled]
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+ teacher = "/home/tlam/deeperfly-projects/octacam/runs/mvt_dinov3/tier1/c6_vitb_warm_5k/model.pth" # held-out-clean warm ViT-B, 4.71 px
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+ n_per_project = 200
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+ transductive = false
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+ agree_px = 6.0
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+ min_views = 3
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+ conf_min = 0.3
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+ weight = 0.5
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+ mask_ratios = []
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+ masked_weight = 1.0
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+ unmasked_weight = 0.5
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+ crop_tightness = [0.75, 1.6]
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+ cache = "../../../cache/unlabeled"
260927_mvt_dinov3b_384_octacam_fly38/fly38.toml ADDED
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+ # fly38 -- the 38 tracked points of a tethered Drosophila: six 5-point legs, two
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+ # antennae, the neck, and a 5-point dorsal-midline abdomen chain (the tergite stripes).
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+ #
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+ # A skeleton is points, edges and point_symmetries -- the same decomposition as SLEAP
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+ # and DeepLabCut -- plus an optional palette (point_colors / edge_colors). The palette
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+ # is decoration, not identity: it draws the points but is kept out of the digest, so
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+ # recoloring never reports a different skeleton.
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+
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+ [skeleton]
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+ name = "fly38"
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+
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+ # The points IN ORDER: channel i of the detector is points[i]. This is the contract
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+ # with the weights.
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+ points = [
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+ "lf_thorax_coxa", "lf_coxa_trochanter", "lf_femur_tibia", "lf_tibia_tarsus", "lf_pretarsus",
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+ "lm_thorax_coxa", "lm_coxa_trochanter", "lm_femur_tibia", "lm_tibia_tarsus", "lm_pretarsus",
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+ "lh_thorax_coxa", "lh_coxa_trochanter", "lh_femur_tibia", "lh_tibia_tarsus", "lh_pretarsus",
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+ "l_antenna",
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+ "rf_thorax_coxa", "rf_coxa_trochanter", "rf_femur_tibia", "rf_tibia_tarsus", "rf_pretarsus",
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+ "rm_thorax_coxa", "rm_coxa_trochanter", "rm_femur_tibia", "rm_tibia_tarsus", "rm_pretarsus",
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+ "rh_thorax_coxa", "rh_coxa_trochanter", "rh_femur_tibia", "rh_tibia_tarsus", "rh_pretarsus",
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+ "r_antenna",
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+ "neck",
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+ "abdomen0", "abdomen1", "abdomen2", "abdomen3", "abdomen4",
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+ ]
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+
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+ # The edges, as pairs of points. The antennae and neck appear in no edge -- tracked
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+ # points with no bone.
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+ edges = [
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+ ["lf_thorax_coxa", "lf_coxa_trochanter"], ["lf_coxa_trochanter", "lf_femur_tibia"],
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+ ["lf_femur_tibia", "lf_tibia_tarsus"], ["lf_tibia_tarsus", "lf_pretarsus"],
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+ ["lm_thorax_coxa", "lm_coxa_trochanter"], ["lm_coxa_trochanter", "lm_femur_tibia"],
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+ ["lm_femur_tibia", "lm_tibia_tarsus"], ["lm_tibia_tarsus", "lm_pretarsus"],
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+ ["lh_thorax_coxa", "lh_coxa_trochanter"], ["lh_coxa_trochanter", "lh_femur_tibia"],
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+ ["lh_femur_tibia", "lh_tibia_tarsus"], ["lh_tibia_tarsus", "lh_pretarsus"],
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+ ["rf_thorax_coxa", "rf_coxa_trochanter"], ["rf_coxa_trochanter", "rf_femur_tibia"],
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+ ["rf_femur_tibia", "rf_tibia_tarsus"], ["rf_tibia_tarsus", "rf_pretarsus"],
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+ ["rm_thorax_coxa", "rm_coxa_trochanter"], ["rm_coxa_trochanter", "rm_femur_tibia"],
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+ ["rm_femur_tibia", "rm_tibia_tarsus"], ["rm_tibia_tarsus", "rm_pretarsus"],
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+ ["rh_thorax_coxa", "rh_coxa_trochanter"], ["rh_coxa_trochanter", "rh_femur_tibia"],
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+ ["rh_femur_tibia", "rh_tibia_tarsus"], ["rh_tibia_tarsus", "rh_pretarsus"],
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+ ["abdomen0", "abdomen1"], ["abdomen1", "abdomen2"], ["abdomen2", "abdomen3"], ["abdomen3", "abdomen4"],
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+ ]
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+
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+ # What each point becomes under a left/right flip. Write each pair once; anything absent
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+ # is on the midline and maps to itself (hence no neck, no abdomen). The loader checks
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+ # the implied mirror against `edges`: applying it must give the edge set back, so a
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+ # wrong side or two joints of one leg exchanged is named rather than trained on silently.
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+ point_symmetries = [
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+ ["lf_thorax_coxa", "rf_thorax_coxa"],
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+ ["lf_coxa_trochanter", "rf_coxa_trochanter"],
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+ ["lf_femur_tibia", "rf_femur_tibia"],
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+ ["lf_tibia_tarsus", "rf_tibia_tarsus"],
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+ ["lf_pretarsus", "rf_pretarsus"],
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+ ["lm_thorax_coxa", "rm_thorax_coxa"],
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+ ["lm_coxa_trochanter", "rm_coxa_trochanter"],
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+ ["lm_femur_tibia", "rm_femur_tibia"],
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+ ["lm_tibia_tarsus", "rm_tibia_tarsus"],
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+ ["lm_pretarsus", "rm_pretarsus"],
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+ ["lh_thorax_coxa", "rh_thorax_coxa"],
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+ ["lh_coxa_trochanter", "rh_coxa_trochanter"],
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+ ["lh_femur_tibia", "rh_femur_tibia"],
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+ ["lh_tibia_tarsus", "rh_tibia_tarsus"],
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+ ["lh_pretarsus", "rh_pretarsus"],
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+ ["l_antenna", "r_antenna"],
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+ ]
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+
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+ # The palette. One #rrggbb per point; a key is a point name or a `*` pattern (an exact
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+ # name beats a pattern). Optional and may be partial -- an unnamed point takes tab10 by
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+ # index. The scheme is anatomical, so it reads at a glance: left = blue, right = red,
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+ # front -> hind lightening within a side; the midline neck and abdomen green. Edges take
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+ # the average of their endpoints, so every leg bone comes out its own limb's color.
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+ [skeleton.point_colors]
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+ "lf_*" = "#0f7399"
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+ "lm_*" = "#1a8daf"
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+ "lh_*" = "#75becb"
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+ l_antenna = "#0a4f6b"
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+ "rf_*" = "#ba1e31"
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+ "rm_*" = "#c9564f"
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+ "rh_*" = "#d58579"
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+ r_antenna = "#8c1525"
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+ neck = "#15a315"
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+ "abdomen*" = "#61e47b"
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+
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+ # A canonical neutral posture (NeuroMechFly's rest pose), one [x, y, z] per point
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+ # in millimeters, with the body center of mass at the origin (x anterior, y the
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+ # left-right axis, z dorsal). It is NOT part of the skeleton's identity (out of the
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+ # digest); it draws the skeleton in 3D and SEEDS labeling: projected through a
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+ # recording's calibration it drops a rough draggable instance into each view when
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+ # nothing else (a prior labeled frame, another view) is available to seed from.
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+ [skeleton.default_pose]
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+ lf_thorax_coxa = [ 0.42966, 0.17200, 0.25226]
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+ lf_coxa_trochanter = [ 0.31028, 0.06883, -0.07688]
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+ lf_femur_tibia = [ 0.85227, 0.42043, 0.20537]
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+ lf_tibia_tarsus = [ 1.05606, 0.65936, -0.20658]
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+ lf_pretarsus = [ 1.45133, 1.02885, -0.58856]
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+ lm_thorax_coxa = [ 0.03366, 0.12500, 0.00026]
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+ lm_coxa_trochanter = [ 0.00831, 0.09367, -0.17620]
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+ lm_femur_tibia = [ 0.11746, 0.70120, 0.30719]
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+ lm_tibia_tarsus = [ 0.23055, 0.96680, -0.29411]
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+ lm_pretarsus = [ 0.38484, 1.49119, -0.73358]
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+ lh_thorax_coxa = [-0.19334, 0.08700, -0.01474]
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+ lh_coxa_trochanter = [-0.27402, 0.09655, -0.19640]
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+ lh_femur_tibia = [-0.64760, 0.63110, 0.32665]
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+ lh_tibia_tarsus = [-0.96496, 0.77982, -0.26073]
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+ lh_pretarsus = [-1.40791, 1.03885, -0.86325]
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+ l_antenna = [ 1.04836, 0.08600, 0.56596]
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+ rf_thorax_coxa = [ 0.42966, -0.17200, 0.25226]
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+ rf_coxa_trochanter = [ 0.31028, -0.06883, -0.07688]
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+ rf_femur_tibia = [ 0.85227, -0.42043, 0.20537]
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+ rf_tibia_tarsus = [ 1.05606, -0.65936, -0.20658]
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+ rf_pretarsus = [ 1.45133, -1.02885, -0.58856]
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+ rm_thorax_coxa = [ 0.03366, -0.12500, 0.00026]
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+ rm_coxa_trochanter = [ 0.00831, -0.09367, -0.17620]
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+ rm_femur_tibia = [ 0.11746, -0.70120, 0.30719]
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+ rm_tibia_tarsus = [ 0.23055, -0.96680, -0.29411]
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+ rm_pretarsus = [ 0.38484, -1.49119, -0.73358]
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+ rh_thorax_coxa = [-0.19334, -0.08700, -0.01474]
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+ rh_coxa_trochanter = [-0.27402, -0.09655, -0.19640]
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+ rh_femur_tibia = [-0.64760, -0.63110, 0.32665]
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+ rh_tibia_tarsus = [-0.96496, -0.77982, -0.26073]
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+ rh_pretarsus = [-1.40791, -1.03885, -0.86325]
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+ r_antenna = [ 1.04836, -0.08600, 0.56596]
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+ neck = [ 0.61936, 0.00000, 0.48296]
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+ abdomen0 = [-0.71698, 0.00000, 0.71444]
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+ abdomen1 = [-0.91268, 0.00000, 0.66169]
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+ abdomen2 = [-1.10060, 0.00000, 0.61850]
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+ abdomen3 = [-1.27163, 0.00000, 0.56551]
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+ abdomen4 = [-1.48737, 0.00000, 0.46364]
260927_mvt_dinov3b_384_octacam_fly38/mvt_dinov3b_384_octacam_fly38.pth ADDED
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+ size 383792459
260927_mvt_dinov3b_384_octacam_fly38/report.json ADDED
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+ {
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+ "projects": {
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+ "9A9_251119_Fly3_003": "/home/tlam/deeperfly-projects/octacam/recordings/9A9_251119_Fly3_003/deeperfly",
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+ "AN07B017_260414_Fly4_003": "/home/tlam/deeperfly-projects/octacam/recordings/AN07B017_260414_Fly4_003/deeperfly",
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+ "AN07B017_260414_Fly4_004": "/home/tlam/deeperfly-projects/octacam/recordings/AN07B017_260414_Fly4_004/deeperfly",
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+ "AN07B017_260414_Fly4_005": "/home/tlam/deeperfly-projects/octacam/recordings/AN07B017_260414_Fly4_005/deeperfly",
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+ "AN19B004_260316_Fly2_003": "/home/tlam/deeperfly-projects/octacam/recordings/AN19B004_260316_Fly2_003/deeperfly",
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+ "ANXXX049_251125_Fly1_003": "/home/tlam/deeperfly-projects/octacam/recordings/ANXXX049_251125_Fly1_003/deeperfly",
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+ "FW_260325_dna01a5_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260325_dna01a5_Fly1_001_label/deeperfly",
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+ "FW_260327_g25_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260327_g25_Fly1_001_label/deeperfly",
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+ "FW_260327_g25_Fly2_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260327_g25_Fly2_001_label/deeperfly",
12
+ "FW_260327_g25_Fly3_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260327_g25_Fly3_001_label/deeperfly",
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+ "FW_260327_g25_Fly5_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260327_g25_Fly5_001_label/deeperfly",
14
+ "FW_260416_CS_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260416_CS_Fly1_001_label/deeperfly",
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+ "FW_260418_cs_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_cs_Fly1_001_label/deeperfly",
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+ "FW_260418_cs_Fly2_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_cs_Fly2_001_label/deeperfly",
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+ "FW_260418_g25i_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_g25i_Fly1_001_label/deeperfly",
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+ "FW_260418_g25i_Fly2_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_g25i_Fly2_001_label/deeperfly",
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+ "FW_260418_g25i_Fly3_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_g25i_Fly3_001_label/deeperfly",
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+ "FW_260418_g25i_Fly4_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260418_g25i_Fly4_001_label/deeperfly",
21
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+ "FW_260423_g25_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260423_g25_Fly1_001_label/deeperfly",
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+ "FW_260424_g25_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260424_g25_Fly1_001_label/deeperfly",
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+ "FW_260507_dfd_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260507_dfd_Fly1_001_label/deeperfly",
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+ "FW_260507_g25_Fly1_002": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260507_g25_Fly1_002/deeperfly",
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+ "FW_260507_g25_Fly2_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260507_g25_Fly2_001_label/deeperfly",
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+ "FW_260507_g25_Fly3_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260507_g25_Fly3_001_label/deeperfly",
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+ "FW_260508_g25_Fly1_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260508_g25_Fly1_001_label/deeperfly",
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+ "FW_260508_g25_Fly3_001_label": "/home/tlam/deeperfly-projects/octacam/recordings/FW_260508_g25_Fly3_001_label/deeperfly",
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+ "IN07B001_260417_Fly3_003": "/home/tlam/deeperfly-projects/octacam/recordings/IN07B001_260417_Fly3_003/deeperfly",
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+ "IN07B001_260417_Fly4_007": "/home/tlam/deeperfly-projects/octacam/recordings/IN07B001_260417_Fly4_007/deeperfly",
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+ "IN07B007_260323_Fly3_002": "/home/tlam/deeperfly-projects/octacam/recordings/IN07B007_260323_Fly3_002/deeperfly",
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+ "IN10B012_260319_Fly1_003": "/home/tlam/deeperfly-projects/octacam/recordings/IN10B012_260319_Fly1_003/deeperfly",
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+ "LTM-MN_260119_Fly3_003": "/home/tlam/deeperfly-projects/octacam/recordings/LTM-MN_260119_Fly3_003/deeperfly",
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+ "LTM-MN_260120_Fly3_003": "/home/tlam/deeperfly-projects/octacam/recordings/LTM-MN_260120_Fly3_003/deeperfly",
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+ "LTM-MN_260120_Fly3_006": "/home/tlam/deeperfly-projects/octacam/recordings/LTM-MN_260120_Fly3_006/deeperfly",
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+ "oldrig_demo": "/home/tlam/deeperfly-projects/octacam/recordings/oldrig_demo/deeperfly",
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+ "scape_260417_IN07B001_Fly3_004": "/home/tlam/deeperfly-projects/octacam/recordings/scape_260417_IN07B001_Fly3_004/deeperfly",
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+ "IN07B001_260417_Fly3_003",
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+ "IN14B011_251126_Fly3_004",
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+ "LTM-MN_251217_Fly1_003",
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+ "oldrig_demo",
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+ "scape_260417_IN07B001_Fly3_004",
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+ "scape_260417_IN07B001_Fly4_006"
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+ }