Rib segmentation + low-RAM nnU-Net inference

[robert-graf]

Adds a rib-labelling pipeline on top of an existing vertebra + spine
segmentation and makes full-body nnU-Net inference survivable on
workstations with modest RAM.

Rib pipeline (TPTBox.segmentation.rib)

• add_ribs_to_vert_spine(vert, spine, rib_seg=None, ct=None, ...) merges
  left/right rib labels into an existing vertebra instance + spine
  subregion segmentation. If no raw rib mask is passed, VibeSeg dataset 12
  is run on the CT; if vert/spine are missing, SPINEPS is invoked. Path
  resolution works from either explicit paths or a BIDS_FILE + dataset
  root.
• Internal assign_ribs_to_vert_segmentation performs deterministic
  cranial→caudal matching with a centroid-based left/right split and a T1
  presence heuristic based on adaptive vertebral spacing.
• Internal split_touching_rib_ccs breaks apart rib CCs that fuse the ribs
  of adjacent vertebrae using a multi-pass erosion strategy (Euclidean →
  standard → direction-restricted), with optional short_cut early exit
  once the expected CC count is reached and optional thread-parallel
  evaluation of splits.
• Re-exported at package level: from TPTBox.segmentation import add_ribs_to_vert_spine.

Low-RAM nnU-Net inference

TPTBox/segmentation/nnUnet_utils/inference_api.py and
VibeSeg/inference_nnunet.py:

• New estimate_peak_ram_mb(shape, num_classes, num_channels) estimates
  the peak allocation of a single-pass nnU-Net run (logits + counts +
  input tensor + output seg, with 1.3× headroom).
• New compute_cpu_chunks_for_ram(...) picks the smallest chunk count
  such that one chunk fits under a target RAM budget.
• run_inference_on_file now checks the estimate against 50 % of system
  RAM and transparently switches to chunked inference before OOM instead
  of only reacting to MemoryError. This was needed for the 0.8 mm
  full-CT model, which previously required ~250 GB of RAM on whole-body
  images.
• _run_inference_patches supports auto-chunking (_cpu_chunks=None)
  with a configurable ram_fraction.

Bug fixes

• np_map_labels: cast max(...) + 1 through int() so a label of
  exactly 255 in a uint8 array no longer overflows the LUT bound.
• np_bbox_binary: accept float values for px_dist (rounded up) so
  callers that pass a spacing-derived distance don't crash.

Documentation + cleanup

• New rib API section in docs/api/segmentation.md and the segmentation
  package README (public API, dependency row, worked example).
• Docstring cleanup in the rib module: module docstrings, full argument
  coverage for add_ribs_to_vert_spine, assign_ribs_to_vert_segmentation,
  split_touching_rib_ccs (including short_cut), and removal of a
  phantom max_span_factor kwarg.
• gui/snapshot_reviewer/review_gui.py: silence ruff ARG001 by
  renaming the unused callback arg to _fam.

[github-actions]

Benchmark comparison

Speed (wall time per call)

baseline a163cab vs head a163cab · python 3.11.16 · 5 repeats + 1 warmup

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 ms are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_load_seg	3.00 ±0.08	2.71 ±0.05	-9.7%	0.000
poi_calc_centroids_nocrop	4.69 ±0.09	4.28 ±0.09	-8.6%	0.000
nii_filter_connected_components	4.64 ±0.07	4.30 ±0.07	-7.3%	0.000
nii_rescale_seg	3.34 ±0.13	3.23 ±0.10	-3.2%	0.059
nii_load_img	11.12 ±0.08	10.77 ±0.04	-3.1%	0.000

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
poi_calc_poi_from_subreg_vert	13.33 ±0.25	12.91 ±0.33	-3.1%	0.019
nii_save	12.24 ±0.20	11.89 ±0.13	-2.9%	0.003
nii_erode_msk	6.08 ±0.09	6.20 ±0.06	+1.9%	0.047
nii_fill_holes	4.34 ±0.05	4.41 ±0.09	+1.8%	0.065
nii_rescale	40.16 ±0.22	39.52 ±0.22	-1.6%	0.001
nii_resample_from_to	42.18 ±0.27	41.65 ±0.21	-1.3%	0.007
nii_dilate_msk	123.52 ±0.68	124.32 ±0.39	+0.7%	0.020
metric_voxels	250463.00 ±0.00	250463.00 ±0.00	+0.0%	—
metric_labels	3.00 ±0.00	3.00 ±0.00	+0.0%	—
metric_foreground_pct	14.51 ±0.00	14.51 ±0.00	+0.0%	—
poi_map_labels	0.22 ±0.01	0.15 ±0.01	-30.4% (noise)	0.000
nii_set_dtype	0.57 ±0.02	0.41 ±0.03	-28.9% (noise)	0.000
poi_reorient	0.46 ±0.02	0.37 ±0.03	-20.6% (noise)	0.001
nii_reorient	0.94 ±0.08	0.76 ±0.04	-19.5% (noise)	0.003
nii_apply_crop	0.73 ±0.05	0.59 ±0.03	-18.8% (noise)	0.001
poi_resample_from_to	0.81 ±0.02	0.66 ±0.06	-18.4% (noise)	0.001
nii_pad_to	0.75 ±0.09	0.63 ±0.04	-16.7% (noise)	0.020
poi_load	1.12 ±0.02	0.94 ±0.04	-15.9% (noise)	0.000
poi_to_global	0.24 ±0.01	0.21 ±0.01	-14.1% (noise)	0.001
nii_extract_label	0.48 ±0.03	0.41 ±0.04	-13.6% (noise)	0.037
nii_map_labels	1.10 ±0.04	0.96 ±0.05	-12.9% (noise)	0.001
poi_local_to_global_arr	0.33 ±0.01	0.29 ±0.02	-11.8% (noise)	0.003
poi_save	0.52 ±0.01	0.46 ±0.05	-11.5% (noise)	0.016
nii_compute_crop	0.34 ±0.02	0.31 ±0.02	-10.1% (noise)	0.009
nii_get_array	0.05 ±0.00	0.05 ±0.00	-9.8% (noise)	0.012
poi_rescale	0.25 ±0.02	0.23 ±0.02	-8.3% (noise)	0.018
nii_get_connected_components	2.09 ±0.03	2.26 ±0.03	+8.1% (noise)	0.000
poi_calc_centroids	2.64 ±0.05	2.50 ±0.05	-5.2% (noise)	0.001
nii_center_of_masses	1.82 ±0.04	1.77 ±0.02	-2.9% (noise)	0.057
nii_unique	0.65 ±0.03	0.66 ±0.02	+2.2% (noise)	0.815
nii_volumes	1.88 ±0.04	1.87 ±0.02	-0.8% (noise)	0.153

ct_2d — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_resample_from_to	7.89 ±0.09	7.31 ±0.19	-7.4%	0.004
nii_rescale	5.52 ±0.22	5.40 ±0.16	-2.0%	0.148
nii_dilate_msk	14.76 ±0.69	14.65 ±0.12	-0.7%	0.319
metric_voxels	3431.00 ±0.00	3431.00 ±0.00	+0.0%	—
metric_labels	3.00 ±0.00	3.00 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
metric_foreground_pct	37.60 ±0.00	37.60 ±0.00	+0.0%	—
poi_map_labels	0.20 ±0.01	0.23 ±0.02	+15.4% (noise)	0.009
nii_get_array	0.02 ±0.00	0.02 ±0.00	-10.6% (noise)	0.006
nii_set_dtype	0.47 ±0.02	0.42 ±0.02	-9.8% (noise)	0.001
nii_load_img	1.72 ±0.08	1.55 ±0.03	-9.8% (noise)	0.003
nii_apply_crop	0.77 ±0.02	0.70 ±0.02	-9.5% (noise)	0.000
nii_reorient	0.95 ±0.04	0.86 ±0.03	-9.5% (noise)	0.002
poi_local_to_global_arr	0.36 ±0.01	0.33 ±0.02	-8.8% (noise)	0.098
poi_rescale	0.29 ±0.03	0.27 ±0.01	-8.3% (noise)	0.037
nii_unique	0.14 ±0.01	0.12 ±0.01	-7.9% (noise)	0.028
nii_fill_holes	0.95 ±0.01	0.88 ±0.02	-7.9% (noise)	0.000
poi_load	1.13 ±0.04	1.04 ±0.03	-7.7% (noise)	0.033
nii_map_labels	0.57 ±0.02	0.53 ±0.03	-7.4% (noise)	0.033
poi_to_global	0.27 ±0.02	0.25 ±0.02	-7.3% (noise)	0.357
nii_erode_msk	1.11 ±0.03	1.03 ±0.03	-7.1% (noise)	0.003
nii_compute_crop	0.16 ±0.01	0.15 ±0.01	-6.7% (noise)	0.021
poi_calc_centroids_nocrop	1.28 ±0.02	1.20 ±0.03	-6.5% (noise)	0.001
nii_get_connected_components	0.71 ±0.05	0.67 ±0.04	-6.2% (noise)	0.231
nii_pad_to	0.64 ±0.03	0.60 ±0.08	-5.9% (noise)	0.881
poi_reorient	0.49 ±0.02	0.47 ±0.02	-4.2% (noise)	0.026
nii_rescale_seg	0.81 ±0.04	0.78 ±0.06	-4.1% (noise)	0.721
nii_extract_label	0.48 ±0.02	0.46 ±0.01	-4.1% (noise)	0.045
poi_save	0.49 ±0.03	0.51 ±0.02	+3.9% (noise)	0.427
nii_volumes	0.31 ±0.03	0.30 ±0.02	-3.9% (noise)	0.172
poi_calc_centroids	1.00 ±0.07	0.96 ±0.04	-3.2% (noise)	0.104
poi_resample_from_to	0.74 ±0.01	0.76 ±0.03	+2.5% (noise)	0.493
nii_filter_connected_components	0.86 ±0.01	0.88 ±0.05	+1.8% (noise)	0.914
nii_load_seg	1.74 ±0.10	1.72 ±0.04	-1.1% (noise)	0.138
nii_save	1.41 ±0.06	1.40 ±0.04	-0.6% (noise)	0.837
nii_center_of_masses	0.22 ±0.01	0.22 ±0.01	-0.4% (noise)	0.266

mri_3d — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_load_seg	3.03 ±0.03	2.88 ±0.12	-4.9%	0.019
poi_calc_centroids	3.02 ±0.04	2.88 ±0.07	-4.9%	0.006
nii_save	9.81 ±0.25	9.41 ±0.12	-4.1%	0.043
nii_rescale_seg	3.23 ±0.07	3.12 ±0.04	-3.4%	0.036
nii_erode_msk	7.65 ±0.15	7.89 ±0.08	+3.1%	0.049

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
poi_calc_centroids_nocrop	8.94 ±0.36	8.71 ±0.19	-2.6%	0.303
nii_load_img	9.07 ±0.10	8.88 ±0.11	-2.1%	0.020
poi_calc_poi_from_subreg_vert	12.01 ±0.26	12.24 ±0.24	+1.9%	0.477
nii_filter_connected_components	4.67 ±0.07	4.71 ±0.02	+0.9%	0.480
nii_rescale	38.19 ±0.18	38.47 ±1.42	+0.7%	0.233
nii_fill_holes	5.43 ±0.21	5.40 ±0.04	-0.7%	0.489
nii_dilate_msk	160.23 ±0.98	161.25 ±0.88	+0.6%	0.064
nii_resample_from_to	40.31 ±0.23	40.10 ±0.72	-0.5%	0.858
metric_voxels	236912.00 ±0.00	236912.00 ±0.00	+0.0%	—
metric_labels	8.00 ±0.00	8.00 ±0.00	+0.0%	—
metric_foreground_pct	18.21 ±0.00	18.21 ±0.00	+0.0%	—
nii_unique	0.73 ±0.02	0.64 ±0.02	-13.1% (noise)	0.002
nii_apply_crop	0.84 ±0.04	0.73 ±0.03	-12.9% (noise)	0.001
nii_extract_label	0.55 ±0.02	0.48 ±0.02	-12.6% (noise)	0.000
poi_to_global	0.27 ±0.02	0.30 ±0.01	+12.2% (noise)	0.010
nii_get_array	0.06 ±0.00	0.05 ±0.00	-11.7% (noise)	0.001
poi_local_to_global_arr	0.31 ±0.01	0.35 ±0.02	+10.8% (noise)	0.012
nii_map_labels	1.10 ±0.04	0.98 ±0.03	-10.1% (noise)	0.002
nii_pad_to	0.81 ±0.02	0.74 ±0.02	-9.3% (noise)	0.000
poi_resample_from_to	0.77 ±0.02	0.84 ±0.04	+8.0% (noise)	0.028
nii_set_dtype	0.61 ±0.06	0.56 ±0.03	-7.1% (noise)	0.454
poi_reorient	0.49 ±0.01	0.52 ±0.02	+5.5% (noise)	0.010
poi_load	2.19 ±0.06	2.30 ±0.10	+5.4% (noise)	0.042
nii_center_of_masses	2.09 ±0.01	2.03 ±0.04	-2.6% (noise)	0.007
nii_volumes	2.05 ±0.04	2.00 ±0.05	-2.1% (noise)	0.159
poi_rescale	0.30 ±0.01	0.29 ±0.01	-2.0% (noise)	0.521
nii_reorient	0.98 ±0.03	0.97 ±0.06	-1.8% (noise)	0.910
poi_save	0.59 ±0.03	0.58 ±0.02	-1.5% (noise)	0.612
nii_compute_crop	0.34 ±0.00	0.35 ±0.03	+0.9% (noise)	0.389
nii_get_connected_components	2.20 ±0.08	2.21 ±0.08	+0.7% (noise)	0.557
poi_map_labels	0.26 ±0.02	0.27 ±0.01	+0.7% (noise)	0.909

mri_2d — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_resample_from_to	7.47 ±0.14	7.71 ±0.02	+3.2%	0.012
nii_rescale	5.36 ±0.11	5.45 ±0.04	+1.7%	0.053
nii_dilate_msk	19.37 ±0.09	19.54 ±0.13	+0.9%	0.019
metric_voxels	3536.00 ±0.00	3536.00 ±0.00	+0.0%	—
metric_labels	7.00 ±0.00	7.00 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
metric_foreground_pct	50.17 ±0.00	50.17 ±0.00	+0.0%	—
poi_to_global	0.24 ±0.01	0.29 ±0.01	+19.2% (noise)	0.000
nii_get_connected_components	0.60 ±0.03	0.70 ±0.03	+16.1% (noise)	0.001
nii_unique	0.12 ±0.01	0.13 ±0.01	+16.1% (noise)	0.015
nii_rescale_seg	0.76 ±0.01	0.88 ±0.05	+15.9% (noise)	0.005
nii_extract_label	0.40 ±0.03	0.46 ±0.01	+15.8% (noise)	0.007
poi_rescale	0.28 ±0.02	0.32 ±0.01	+12.5% (noise)	0.018
nii_map_labels	0.48 ±0.01	0.53 ±0.02	+11.8% (noise)	0.004
nii_reorient	0.81 ±0.03	0.90 ±0.03	+11.3% (noise)	0.000
poi_calc_centroids_nocrop	1.37 ±0.04	1.52 ±0.05	+10.5% (noise)	0.001
nii_set_dtype	0.39 ±0.01	0.43 ±0.01	+10.5% (noise)	0.000
nii_volumes	0.45 ±0.02	0.49 ±0.01	+8.6% (noise)	0.005
poi_calc_centroids	1.10 ±0.02	1.20 ±0.07	+8.5% (noise)	0.017
poi_save	0.62 ±0.03	0.57 ±0.04	-8.4% (noise)	0.267
nii_compute_crop	0.14 ±0.01	0.16 ±0.01	+8.4% (noise)	0.149
poi_reorient	0.50 ±0.02	0.54 ±0.02	+8.2% (noise)	0.057
nii_load_seg	1.68 ±0.05	1.81 ±0.02	+7.6% (noise)	0.001
nii_load_img	1.44 ±0.05	1.55 ±0.04	+7.5% (noise)	0.045
nii_apply_crop	0.66 ±0.03	0.70 ±0.02	+7.2% (noise)	0.012
nii_save	1.36 ±0.03	1.45 ±0.04	+7.2% (noise)	0.001
nii_erode_msk	1.28 ±0.02	1.36 ±0.04	+6.6% (noise)	0.006
poi_local_to_global_arr	0.32 ±0.01	0.34 ±0.01	+6.2% (noise)	0.030
poi_resample_from_to	0.83 ±0.02	0.87 ±0.02	+5.0% (noise)	0.077
nii_filter_connected_components	0.84 ±0.03	0.88 ±0.05	+5.0% (noise)	0.205
nii_fill_holes	1.08 ±0.03	1.13 ±0.03	+4.8% (noise)	0.016
poi_load	1.98 ±0.09	2.07 ±0.05	+4.6% (noise)	0.082
nii_pad_to	0.55 ±0.04	0.58 ±0.06	+3.9% (noise)	0.146
poi_map_labels	0.26 ±0.01	0.25 ±0.01	-1.1% (noise)	0.769
nii_center_of_masses	0.40 ±0.02	0.40 ±0.01	+0.9% (noise)	0.294
nii_get_array	0.02 ±0.00	0.02 ±0.00	-0.2% (noise)	0.875

Gate: a measurement fails when the baseline is ≥ 1 ms, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

Memory (peak RSS growth per call)

baseline a163cab vs head a163cab · python 3.11.16 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.90 MiB

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 MiB are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_img	3.57 ±0.00	3.53 ±0.00	-1.1%	—
nii_set_dtype	5.23 ±0.00	5.27 ±0.00	+0.7%	—
nii_pad_to	5.41 ±0.00	5.45 ±0.00	+0.7%	—
nii_extract_label	5.42 ±0.00	5.46 ±0.00	+0.7%	—
nii_map_labels	5.48 ±0.00	5.52 ±0.00	+0.7%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_apply_crop	5.86 ±0.00	5.89 ±0.00	+0.7%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.95 ±0.00	+0.7%	—
nii_rescale_seg	5.93 ±0.00	5.97 ±0.00	+0.7%	—
poi_calc_centroids	6.04 ±0.00	6.08 ±0.00	+0.6%	—
nii_fill_holes	6.27 ±0.00	6.31 ±0.00	+0.6%	—
nii_get_connected_components	6.61 ±0.00	6.64 ±0.00	+0.6%	—
nii_filter_connected_components	6.86 ±0.00	6.89 ±0.00	+0.6%	—
poi_calc_poi_from_subreg_vert	7.10 ±0.00	7.14 ±0.00	+0.6%	—
nii_erode_msk	5.91 ±0.00	5.93 ±0.00	+0.3%	—
nii_dilate_msk	5.92 ±0.00	5.93 ±0.00	+0.3%	—
nii_load_seg	6.00 ±0.00	6.00 ±0.00	+0.0%	—
nii_save	3.71 ±0.00	3.71 ±0.00	+0.0%	—
nii_reorient	5.89 ±0.00	5.89 ±0.00	+0.0%	—
nii_rescale	6.16 ±0.00	6.16 ±0.00	+0.0%	—
nii_resample_from_to	6.29 ±0.00	6.29 ±0.00	+0.0%	—
nii_volumes	3.53 ±0.00	3.53 ±0.00	+0.0%	—
nii_center_of_masses	3.28 ±0.03	3.28 ±0.00	+0.0%	0.374
poi_reorient	3.84 ±0.00	3.84 ±0.00	+0.0%	—
poi_to_global	3.09 ±0.00	3.09 ±0.00	+0.0%	—
poi_resample_from_to	5.27 ±0.00	5.27 ±0.00	+0.0%	—
metric_voxels	250463.00 ±0.00	250463.00 ±0.00	+0.0%	—
metric_labels	3.00 ±0.00	3.00 ±0.00	+0.0%	—
metric_foreground_pct	14.51 ±0.00	14.51 ±0.00	+0.0%	—
nii_get_array	1.65 ±0.00	1.65 ±0.00	+0.0% (noise)	—
nii_compute_crop	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
nii_unique	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
poi_rescale	2.61 ±0.00	2.61 ±0.00	+0.0% (noise)	—
poi_local_to_global_arr	2.96 ±0.00	2.96 ±0.00	+0.0% (noise)	—
poi_save	1.41 ±0.00	1.41 ±0.00	+0.0% (noise)	—
poi_map_labels	1.78 ±0.00	1.78 ±0.00	+0.0% (noise)	—
poi_load	1.62 ±0.00	1.62 ±0.00	+0.0% (noise)	—

ct_2d — shape (73, 47, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_img	3.50 ±0.00	3.46 ±0.00	-1.0%	—
nii_set_dtype	5.16 ±0.00	5.20 ±0.00	+0.8%	—
nii_pad_to	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_extract_label	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_map_labels	5.41 ±0.00	5.45 ±0.00	+0.7%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_apply_crop	5.79 ±0.00	5.83 ±0.00	+0.7%	—
nii_rescale_seg	5.87 ±0.00	5.91 ±0.00	+0.7%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.95 ±0.00	+0.7%	—
poi_calc_centroids	5.98 ±0.00	6.02 ±0.00	+0.7%	—
nii_fill_holes	6.20 ±0.00	6.24 ±0.00	+0.6%	—
nii_get_connected_components	6.54 ±0.00	6.58 ±0.00	+0.6%	—
nii_filter_connected_components	6.79 ±0.00	6.83 ±0.00	+0.6%	—
nii_erode_msk	5.85 ±0.00	5.86 ±0.00	+0.3%	—
nii_dilate_msk	5.85 ±0.00	5.87 ±0.00	+0.3%	—
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.1%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.0%	—
nii_resample_from_to	6.22 ±0.00	6.22 ±0.00	+0.0%	—
nii_volumes	3.46 ±0.00	3.46 ±0.00	+0.0%	—
nii_center_of_masses	3.21 ±0.00	3.21 ±0.00	+0.0%	—
poi_reorient	3.77 ±0.00	3.77 ±0.00	+0.0%	—
poi_to_global	3.02 ±0.00	3.02 ±0.00	+0.0%	—
poi_resample_from_to	5.20 ±0.00	5.20 ±0.00	+0.0%	—
metric_voxels	3431.00 ±0.00	3431.00 ±0.00	+0.0%	—
metric_labels	3.00 ±0.00	3.00 ±0.00	+0.0%	—
metric_foreground_pct	37.60 ±0.00	37.60 ±0.00	+0.0%	—
nii_get_array	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
nii_compute_crop	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
nii_unique	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
poi_rescale	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
poi_local_to_global_arr	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
poi_save	1.34 ±0.00	1.34 ±0.00	+0.0% (noise)	—
poi_map_labels	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
poi_load	1.55 ±0.00	1.55 ±0.00	+0.0% (noise)	—

mri_3d — shape (68, 52, 67)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_img	3.56 ±0.00	3.53 ±0.00	-1.0%	—
nii_set_dtype	5.23 ±0.00	5.27 ±0.00	+0.7%	—
nii_pad_to	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_extract_label	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_map_labels	5.41 ±0.00	5.45 ±0.00	+0.7%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_apply_crop	5.79 ±0.00	5.83 ±0.00	+0.7%	—
poi_calc_centroids_nocrop	5.85 ±0.00	5.89 ±0.00	+0.7%	—
nii_rescale_seg	5.87 ±0.00	5.91 ±0.00	+0.7%	—
poi_calc_centroids	5.98 ±0.00	6.02 ±0.00	+0.7%	—
nii_fill_holes	6.20 ±0.00	6.24 ±0.00	+0.6%	—
nii_get_connected_components	6.54 ±0.00	6.58 ±0.00	+0.6%	—
nii_filter_connected_components	6.79 ±0.00	6.83 ±0.00	+0.6%	—
poi_calc_poi_from_subreg_vert	7.10 ±0.00	7.14 ±0.00	+0.6%	—
nii_erode_msk	5.85 ±0.00	5.86 ±0.00	+0.3%	—
nii_dilate_msk	5.85 ±0.00	5.87 ±0.00	+0.3%	—
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.1%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.0%	—
nii_resample_from_to	6.22 ±0.00	6.22 ±0.00	+0.0%	—
nii_volumes	3.46 ±0.00	3.46 ±0.00	+0.0%	—
nii_center_of_masses	3.21 ±0.00	3.21 ±0.00	+0.0%	—
poi_reorient	3.77 ±0.00	3.77 ±0.00	+0.0%	—
poi_to_global	3.02 ±0.00	3.02 ±0.00	+0.0%	—
poi_resample_from_to	5.20 ±0.00	5.20 ±0.00	+0.0%	—
metric_voxels	236912.00 ±0.00	236912.00 ±0.00	+0.0%	—
metric_labels	8.00 ±0.00	8.00 ±0.00	+0.0%	—
metric_foreground_pct	18.21 ±0.00	18.21 ±0.00	+0.0%	—
nii_get_array	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
nii_compute_crop	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
nii_unique	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
poi_rescale	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
poi_local_to_global_arr	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
poi_save	1.40 ±0.00	1.40 ±0.00	+0.0% (noise)	—
poi_map_labels	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
poi_load	1.55 ±0.00	1.55 ±0.00	+0.0% (noise)	—

mri_2d — shape (68, 52, 1)

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_img	3.56 ±0.00	3.53 ±0.00	-1.0%	—
nii_set_dtype	5.23 ±0.00	5.27 ±0.00	+0.7%	—
nii_pad_to	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_extract_label	5.35 ±0.00	5.39 ±0.00	+0.7%	—
nii_map_labels	5.41 ±0.00	5.45 ±0.00	+0.7%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_apply_crop	5.79 ±0.00	5.83 ±0.00	+0.7%	—
nii_rescale_seg	5.87 ±0.00	5.91 ±0.00	+0.7%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.95 ±0.00	+0.7%	—
poi_calc_centroids	5.98 ±0.00	6.02 ±0.00	+0.7%	—
nii_fill_holes	6.20 ±0.00	6.24 ±0.00	+0.6%	—
nii_get_connected_components	6.54 ±0.00	6.58 ±0.00	+0.6%	—
nii_filter_connected_components	6.79 ±0.00	6.83 ±0.00	+0.6%	—
nii_erode_msk	5.85 ±0.00	5.86 ±0.00	+0.3%	—
nii_dilate_msk	5.85 ±0.00	5.87 ±0.00	+0.3%	—
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.1%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.0%	—
nii_resample_from_to	6.22 ±0.00	6.22 ±0.00	+0.0%	—
nii_volumes	3.46 ±0.00	3.46 ±0.00	+0.0%	—
nii_center_of_masses	3.21 ±0.00	3.21 ±0.00	+0.0%	—
poi_reorient	3.77 ±0.00	3.77 ±0.00	+0.0%	—
poi_to_global	3.02 ±0.00	3.02 ±0.00	+0.0%	—
poi_resample_from_to	5.20 ±0.00	5.20 ±0.00	+0.0%	—
metric_voxels	3536.00 ±0.00	3536.00 ±0.00	+0.0%	—
metric_labels	7.00 ±0.00	7.00 ±0.00	+0.0%	—
metric_foreground_pct	50.17 ±0.00	50.17 ±0.00	+0.0%	—
nii_get_array	1.59 ±0.00	1.59 ±0.00	+0.0% (noise)	—
nii_compute_crop	2.84 ±0.00	2.84 ±0.00	+0.0% (noise)	—
nii_unique	2.90 ±0.00	2.90 ±0.00	+0.0% (noise)	—
poi_rescale	2.54 ±0.00	2.54 ±0.00	+0.0% (noise)	—
poi_local_to_global_arr	2.89 ±0.00	2.89 ±0.00	+0.0% (noise)	—
poi_save	1.40 ±0.00	1.40 ±0.00	+0.0% (noise)	—
poi_map_labels	1.71 ±0.00	1.71 ±0.00	+0.0% (noise)	—
poi_load	1.55 ±0.00	1.55 ±0.00	+0.0% (noise)	—

Gate: a measurement fails when the baseline is ≥ 1 MiB, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.