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 8cd1efe vs head 8cd1efe · 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_fill_holes	4.66 ±0.08	4.81 ±0.03	+3.3%	0.049
nii_erode_msk	6.02 ±0.07	6.16 ±0.05	+2.4%	0.031
nii_dilate_msk	120.51 ±0.86	119.43 ±0.20	-0.9%	0.015
poi_calc_centroids_nocrop	4.47 ±0.09	4.50 ±0.05	+0.8%	0.747
poi_calc_poi_from_subreg_vert	11.79 ±0.15	11.70 ±0.18	-0.7%	0.774

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_save	11.63 ±0.06	11.70 ±0.12	+0.6%	0.956
nii_filter_connected_components	4.34 ±0.05	4.32 ±0.05	-0.5%	0.908
nii_load_img	11.85 ±0.04	11.80 ±0.06	-0.4%	0.093
nii_resample_from_to	41.59 ±0.16	41.74 ±0.23	+0.4%	0.479
nii_rescale_seg	3.17 ±0.06	3.16 ±0.10	-0.3%	0.999
nii_rescale	39.92 ±0.42	39.86 ±0.16	-0.1%	0.609
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_reorient	0.35 ±0.02	0.44 ±0.03	+24.4% (noise)	0.001
poi_to_global	0.19 ±0.02	0.23 ±0.02	+22.2% (noise)	0.019
poi_map_labels	0.18 ±0.02	0.21 ±0.01	+18.1% (noise)	0.018
nii_compute_crop	0.28 ±0.03	0.33 ±0.03	+17.8% (noise)	0.090
nii_extract_label	0.43 ±0.04	0.36 ±0.03	-17.7% (noise)	0.032
poi_resample_from_to	0.59 ±0.03	0.65 ±0.04	+11.2% (noise)	0.006
nii_set_dtype	0.43 ±0.05	0.48 ±0.02	+10.9% (noise)	0.238
poi_save	0.41 ±0.02	0.45 ±0.01	+9.5% (noise)	0.001
poi_rescale	0.20 ±0.02	0.21 ±0.03	+5.4% (noise)	0.568
nii_apply_crop	0.58 ±0.05	0.55 ±0.02	-5.2% (noise)	0.334
nii_get_array	0.05 ±0.00	0.05 ±0.00	+5.0% (noise)	0.328
nii_load_seg	2.83 ±0.08	2.73 ±0.11	-3.8% (noise)	0.469
poi_load	0.90 ±0.03	0.93 ±0.02	+3.6% (noise)	0.028
nii_pad_to	0.60 ±0.04	0.61 ±0.03	+1.9% (noise)	0.775
nii_reorient	0.77 ±0.03	0.78 ±0.04	+1.9% (noise)	0.683
nii_map_labels	0.89 ±0.05	0.88 ±0.07	-1.6% (noise)	0.908
nii_center_of_masses	1.84 ±0.03	1.82 ±0.01	-1.1% (noise)	0.157
poi_calc_centroids	2.55 ±0.03	2.57 ±0.08	+1.1% (noise)	0.735
nii_get_connected_components	2.14 ±0.05	2.12 ±0.03	-1.0% (noise)	0.812
nii_unique	0.62 ±0.01	0.63 ±0.05	+0.8% (noise)	0.902
nii_volumes	1.93 ±0.03	1.95 ±0.03	+0.6% (noise)	0.698
poi_local_to_global_arr	0.27 ±0.01	0.27 ±0.02	+0.4% (noise)	0.620

ct_2d — shape (73, 47, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_dilate_msk	13.98 ±0.20	13.71 ±0.03	-2.0%	0.019
nii_resample_from_to	7.29 ±0.17	7.43 ±0.13	+1.9%	0.091
nii_rescale	5.63 ±0.10	5.66 ±0.23	+0.5%	0.707
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%	—
nii_get_array	0.02 ±0.00	0.02 ±0.00	+18.7% (noise)	0.133
nii_unique	0.13 ±0.01	0.15 ±0.00	+8.5% (noise)	0.051
poi_resample_from_to	0.76 ±0.03	0.80 ±0.08	+6.3% (noise)	0.078
poi_load	1.02 ±0.01	1.07 ±0.11	+5.5% (noise)	0.185
poi_map_labels	0.22 ±0.01	0.23 ±0.02	+5.1% (noise)	0.257
nii_apply_crop	0.70 ±0.02	0.73 ±0.02	+5.0% (noise)	0.224
nii_reorient	0.83 ±0.03	0.87 ±0.03	+5.0% (noise)	0.013
poi_save	0.52 ±0.01	0.54 ±0.02	+4.4% (noise)	0.160
nii_rescale_seg	0.82 ±0.01	0.79 ±0.03	-3.5% (noise)	0.565
poi_rescale	0.27 ±0.01	0.28 ±0.01	+2.6% (noise)	0.096
nii_get_connected_components	0.70 ±0.02	0.68 ±0.01	-2.2% (noise)	0.558
nii_center_of_masses	0.23 ±0.01	0.24 ±0.01	+2.2% (noise)	0.205
nii_filter_connected_components	0.88 ±0.04	0.86 ±0.03	-2.1% (noise)	0.762
nii_pad_to	0.61 ±0.02	0.62 ±0.02	+2.1% (noise)	0.083
nii_set_dtype	0.42 ±0.02	0.43 ±0.02	+1.8% (noise)	0.392
nii_load_img	1.52 ±0.03	1.55 ±0.04	+1.7% (noise)	0.047
nii_fill_holes	0.86 ±0.08	0.85 ±0.01	-1.6% (noise)	0.259
nii_save	1.44 ±0.04	1.42 ±0.04	-1.6% (noise)	0.502
poi_calc_centroids	0.94 ±0.00	0.95 ±0.03	+1.5% (noise)	0.257
nii_erode_msk	0.97 ±0.02	0.99 ±0.06	+1.4% (noise)	0.505
nii_map_labels	0.52 ±0.03	0.52 ±0.02	-1.4% (noise)	0.374
nii_compute_crop	0.17 ±0.01	0.17 ±0.01	-1.1% (noise)	0.954
poi_calc_centroids_nocrop	1.15 ±0.04	1.14 ±0.01	-1.1% (noise)	0.289
poi_local_to_global_arr	0.29 ±0.01	0.30 ±0.01	+1.0% (noise)	0.995
nii_extract_label	0.47 ±0.01	0.47 ±0.01	-0.8% (noise)	0.301
poi_reorient	0.49 ±0.02	0.49 ±0.01	+0.5% (noise)	0.622
nii_volumes	0.31 ±0.01	0.31 ±0.01	+0.3% (noise)	0.524
poi_to_global	0.26 ±0.03	0.26 ±0.01	-0.1% (noise)	0.594
nii_load_seg	1.72 ±0.06	1.72 ±0.04	+0.1% (noise)	0.643

mri_3d — shape (68, 52, 67)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
poi_calc_poi_from_subreg_vert	11.05 ±0.11	10.80 ±0.11	-2.3%	0.023
nii_fill_holes	5.62 ±0.06	5.51 ±0.03	-1.9%	0.006
nii_rescale_seg	3.17 ±0.04	3.11 ±0.03	-1.8%	0.051
poi_calc_centroids_nocrop	9.23 ±0.09	9.07 ±0.03	-1.7%	0.029
nii_dilate_msk	155.18 ±0.26	152.71 ±0.58	-1.6%	0.000

… 31 more measurements

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_load_seg	3.01 ±0.02	2.97 ±0.08	-1.2%	0.188
nii_load_img	9.69 ±0.07	9.58 ±0.08	-1.1%	0.345
nii_filter_connected_components	4.62 ±0.04	4.58 ±0.06	-0.9%	0.484
nii_resample_from_to	39.44 ±0.70	39.25 ±0.37	-0.5%	0.450
nii_rescale	37.41 ±0.27	37.28 ±0.35	-0.4%	0.911
nii_save	9.58 ±0.11	9.59 ±0.13	+0.2%	0.504
nii_erode_msk	7.59 ±0.06	7.60 ±0.06	+0.2%	0.765
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	0.04 ±0.00	0.06 ±0.00	+31.9% (noise)	0.002
nii_set_dtype	0.57 ±0.03	0.52 ±0.02	-7.6% (noise)	0.092
poi_rescale	0.31 ±0.01	0.33 ±0.01	+6.2% (noise)	0.009
poi_local_to_global_arr	0.29 ±0.01	0.31 ±0.01	+5.6% (noise)	0.072
nii_pad_to	0.76 ±0.05	0.80 ±0.02	+4.9% (noise)	0.047
poi_resample_from_to	0.82 ±0.05	0.79 ±0.04	-4.2% (noise)	0.261
poi_load	2.09 ±0.02	2.17 ±0.02	+4.2% (noise)	0.000
nii_map_labels	1.05 ±0.03	1.01 ±0.02	-3.9% (noise)	0.012
nii_reorient	0.90 ±0.02	0.93 ±0.06	+3.7% (noise)	0.165
nii_apply_crop	0.76 ±0.02	0.78 ±0.05	+3.3% (noise)	0.979
poi_save	0.61 ±0.02	0.59 ±0.02	-3.0% (noise)	0.093
poi_reorient	0.51 ±0.02	0.53 ±0.01	+2.8% (noise)	0.061
nii_compute_crop	0.36 ±0.01	0.35 ±0.01	-2.7% (noise)	0.076
nii_extract_label	0.51 ±0.02	0.49 ±0.02	-2.6% (noise)	0.362
poi_to_global	0.31 ±0.01	0.31 ±0.01	+1.5% (noise)	0.637
poi_map_labels	0.27 ±0.01	0.28 ±0.01	+1.5% (noise)	0.602
poi_calc_centroids	2.91 ±0.02	2.87 ±0.04	-1.2% (noise)	0.242
nii_get_connected_components	2.10 ±0.01	2.12 ±0.03	+0.6% (noise)	0.752
nii_center_of_masses	2.09 ±0.02	2.10 ±0.02	+0.5% (noise)	0.635
nii_unique	0.61 ±0.01	0.61 ±0.06	-0.2% (noise)	0.379
nii_volumes	2.05 ±0.03	2.05 ±0.01	+0.2% (noise)	0.927

mri_2d — shape (68, 52, 1)

Measurement	baseline ms (median ±½·range)	head ms (median ±½·range)	Δ %	p
nii_rescale	5.67 ±0.05	5.43 ±0.07	-4.4%	0.000
nii_resample_from_to	7.17 ±0.10	7.39 ±0.09	+2.9%	0.013
nii_dilate_msk	18.37 ±0.05	18.13 ±0.05	-1.3%	0.000
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%	—
nii_get_array	0.02 ±0.00	0.02 ±0.01	+16.9% (noise)	0.642
nii_erode_msk	1.17 ±0.02	1.24 ±0.03	+5.4% (noise)	0.007
nii_reorient	0.85 ±0.03	0.81 ±0.02	-4.8% (noise)	0.087
nii_extract_label	0.44 ±0.01	0.46 ±0.02	+4.1% (noise)	0.037
nii_load_seg	1.64 ±0.03	1.71 ±0.06	+4.0% (noise)	0.102
nii_center_of_masses	0.42 ±0.01	0.41 ±0.01	-3.7% (noise)	0.164
poi_local_to_global_arr	0.28 ±0.01	0.29 ±0.01	+3.2% (noise)	0.210
poi_calc_centroids	1.16 ±0.02	1.12 ±0.04	-3.1% (noise)	0.683
nii_get_connected_components	0.69 ±0.02	0.67 ±0.03	-3.0% (noise)	0.221
nii_unique	0.15 ±0.01	0.14 ±0.01	-2.9% (noise)	0.508
nii_volumes	0.47 ±0.01	0.46 ±0.01	-2.6% (noise)	0.226
nii_apply_crop	0.71 ±0.01	0.73 ±0.02	+2.5% (noise)	0.891
poi_map_labels	0.26 ±0.01	0.26 ±0.01	+2.4% (noise)	0.083
nii_rescale_seg	0.80 ±0.02	0.79 ±0.03	-2.3% (noise)	0.298
poi_resample_from_to	0.76 ±0.02	0.75 ±0.03	-2.2% (noise)	0.367
nii_compute_crop	0.16 ±0.00	0.16 ±0.01	-2.2% (noise)	0.252
poi_reorient	0.52 ±0.02	0.50 ±0.02	-2.1% (noise)	0.186
nii_set_dtype	0.43 ±0.02	0.42 ±0.00	-2.1% (noise)	0.417
nii_save	1.41 ±0.04	1.38 ±0.06	-2.1% (noise)	0.557
nii_filter_connected_components	0.90 ±0.03	0.88 ±0.03	-1.8% (noise)	0.941
poi_calc_centroids_nocrop	1.35 ±0.01	1.37 ±0.03	+1.6% (noise)	0.432
nii_fill_holes	1.07 ±0.03	1.05 ±0.09	-1.4% (noise)	0.382
poi_load	1.90 ±0.05	1.93 ±0.01	+1.2% (noise)	0.499
poi_save	0.58 ±0.04	0.57 ±0.01	-0.6% (noise)	0.970
nii_load_img	1.51 ±0.08	1.50 ±0.04	-0.6% (noise)	0.900
nii_map_labels	0.52 ±0.02	0.52 ±0.02	-0.5% (noise)	0.935
poi_to_global	0.29 ±0.01	0.29 ±0.02	-0.5% (noise)	0.278
nii_pad_to	0.60 ±0.01	0.60 ±0.02	+0.5% (noise)	0.656
poi_rescale	0.31 ±0.01	0.31 ±0.02	+0.2% (noise)	0.414

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 8cd1efe vs head 8cd1efe · 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_rescale_seg	5.93 ±0.00	5.93 ±0.00	+0.1%	—
nii_rescale	6.15 ±0.00	6.16 ±0.00	+0.1%	—
poi_to_global	3.09 ±0.00	3.09 ±0.00	+0.1%	—
nii_resample_from_to	6.28 ±0.00	6.29 ±0.00	+0.1%	—
nii_center_of_masses	3.28 ±0.00	3.28 ±0.00	+0.1%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_volumes	3.53 ±0.00	3.53 ±0.00	+0.1%	—
nii_save	3.71 ±0.00	3.72 ±0.00	+0.1%	—
poi_reorient	3.84 ±0.00	3.84 ±0.00	+0.1%	—
nii_set_dtype	5.23 ±0.00	5.23 ±0.00	+0.1%	—
nii_pad_to	5.41 ±0.00	5.42 ±0.00	+0.1%	—
nii_extract_label	5.42 ±0.00	5.42 ±0.00	+0.1%	—
nii_map_labels	5.48 ±0.00	5.48 ±0.00	+0.1%	—
nii_apply_crop	5.86 ±0.00	5.86 ±0.00	+0.1%	—
nii_reorient	5.89 ±0.00	5.90 ±0.00	+0.1%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.92 ±0.00	+0.1%	—
nii_dilate_msk	5.92 ±0.00	5.92 ±0.00	+0.1%	—
poi_calc_centroids	6.04 ±0.00	6.05 ±0.00	+0.1%	—
nii_fill_holes	6.27 ±0.00	6.27 ±0.00	+0.1%	—
nii_get_connected_components	6.61 ±0.00	6.61 ±0.00	+0.1%	—
nii_filter_connected_components	6.86 ±0.00	6.86 ±0.00	+0.1%	—
nii_load_img	3.57 ±0.00	3.57 ±0.00	+0.0%	—
nii_load_seg	6.00 ±0.00	6.00 ±0.00	+0.0%	—
nii_erode_msk	5.93 ±0.00	5.93 ±0.00	+0.0%	—
poi_resample_from_to	5.27 ±0.00	5.27 ±0.00	+0.0%	—
poi_calc_poi_from_subreg_vert	7.10 ±0.00	7.10 ±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	1.66 ±0.00	+0.2% (noise)	—
poi_rescale	2.61 ±0.00	2.61 ±0.00	+0.1% (noise)	—
poi_local_to_global_arr	2.96 ±0.00	2.96 ±0.00	+0.1% (noise)	—
nii_unique	2.96 ±0.00	2.97 ±0.00	+0.1% (noise)	—
nii_compute_crop	2.90 ±0.00	2.90 ±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_rescale_seg	5.86 ±0.00	5.86 ±0.00	+0.1%	—
nii_erode_msk	5.87 ±0.00	5.86 ±0.00	-0.1%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.1%	—
nii_resample_from_to	6.21 ±0.00	6.21 ±0.00	+0.1%	—
nii_load_img	3.50 ±0.00	3.50 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.0%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_set_dtype	5.16 ±0.00	5.16 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_apply_crop	5.79 ±0.00	5.79 ±0.00	+0.0%	—
nii_pad_to	5.35 ±0.00	5.35 ±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%	—
nii_extract_label	5.35 ±0.00	5.35 ±0.00	+0.0%	—
nii_map_labels	5.41 ±0.00	5.41 ±0.00	+0.0%	—
nii_dilate_msk	5.85 ±0.00	5.85 ±0.00	+0.0%	—
nii_fill_holes	6.20 ±0.00	6.20 ±0.00	+0.0%	—
nii_get_connected_components	6.54 ±0.00	6.54 ±0.00	+0.0%	—
nii_filter_connected_components	6.79 ±0.00	6.79 ±0.00	+0.0%	—
poi_calc_centroids	5.98 ±0.00	5.98 ±0.00	+0.0%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.91 ±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_rescale_seg	5.86 ±0.00	5.86 ±0.00	+0.1%	—
nii_erode_msk	5.87 ±0.00	5.86 ±0.00	-0.1%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.1%	—
nii_resample_from_to	6.21 ±0.00	6.21 ±0.00	+0.1%	—
nii_load_img	3.56 ±0.00	3.56 ±0.00	+0.0%	—

… 31 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.0%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_set_dtype	5.23 ±0.00	5.23 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_apply_crop	5.79 ±0.00	5.79 ±0.00	+0.0%	—
nii_pad_to	5.35 ±0.00	5.35 ±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%	—
nii_extract_label	5.35 ±0.00	5.35 ±0.00	+0.0%	—
nii_map_labels	5.41 ±0.00	5.41 ±0.00	+0.0%	—
nii_dilate_msk	5.85 ±0.00	5.85 ±0.00	+0.0%	—
nii_fill_holes	6.20 ±0.00	6.20 ±0.00	+0.0%	—
nii_get_connected_components	6.54 ±0.00	6.54 ±0.00	+0.0%	—
nii_filter_connected_components	6.79 ±0.00	6.79 ±0.00	+0.0%	—
poi_calc_centroids	5.98 ±0.00	5.98 ±0.00	+0.0%	—
poi_calc_centroids_nocrop	5.85 ±0.00	5.85 ±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%	—
poi_calc_poi_from_subreg_vert	7.10 ±0.00	7.10 ±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_rescale_seg	5.86 ±0.00	5.86 ±0.00	+0.1%	—
nii_erode_msk	5.87 ±0.00	5.86 ±0.00	-0.1%	—
nii_rescale	6.09 ±0.00	6.09 ±0.00	+0.1%	—
nii_resample_from_to	6.21 ±0.00	6.21 ±0.00	+0.1%	—
nii_load_img	3.56 ±0.00	3.56 ±0.00	+0.0%	—

… 30 more measurements

Measurement	baseline MiB (median ±½·range)	head MiB (median ±½·range)	Δ %	p
nii_load_seg	5.93 ±0.00	5.93 ±0.00	+0.0%	—
nii_save	3.65 ±0.00	3.65 ±0.00	+0.0%	—
nii_set_dtype	5.23 ±0.00	5.23 ±0.00	+0.0%	—
nii_reorient	5.83 ±0.00	5.83 ±0.00	+0.0%	—
nii_apply_crop	5.79 ±0.00	5.79 ±0.00	+0.0%	—
nii_pad_to	5.35 ±0.00	5.35 ±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%	—
nii_extract_label	5.35 ±0.00	5.35 ±0.00	+0.0%	—
nii_map_labels	5.41 ±0.00	5.41 ±0.00	+0.0%	—
nii_dilate_msk	5.85 ±0.00	5.85 ±0.00	+0.0%	—
nii_fill_holes	6.20 ±0.00	6.20 ±0.00	+0.0%	—
nii_get_connected_components	6.54 ±0.00	6.54 ±0.00	+0.0%	—
nii_filter_connected_components	6.79 ±0.00	6.79 ±0.00	+0.0%	—
poi_calc_centroids	5.98 ±0.00	5.98 ±0.00	+0.0%	—
poi_calc_centroids_nocrop	5.91 ±0.00	5.91 ±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.