Add batch-wide histogram aggregation, Multi-Otsu thresholding, and QC sweep report

[Copilot]

Enables batchwide threshold optimization for SPIM segmentation: since acquisition parameters are constant within a batch, a single threshold should be computed from all subjects together rather than per-subject. Adds a pipeline from per-subject histogram → batch aggregation → Multi-Otsu → visual QC sweep across all subjects.

New rules (segmentation.smk)

• compute_spim_histogram — computes intensity histogram from raw SPIM channel at an arbitrary pyramid level via Dask; saves counts + bin_edges as .npz
• aggregate_histograms — sums per-subject .npz histograms into a single batch histogram (group datatype output)
• multiotsu_from_batch_histogram — applies percentile-range filtering on the aggregated histogram, then runs Multi-Otsu; outputs thresholds.tsv + thresholds.png

New rule (qc.smk)

• qc_batch_otsu_threshold_sweep — group-level HTML report: sweeps threshold values, showing one mid-volume 2D crop per subject as columns, so the user can immediately see whether a threshold generalises across the batch. Batch histogram PNG is embedded at the top.

New target rule (Snakefile)

• all_batch_otsu_hist_qc — triggers all batchotsuthreshqc.html reports for every stains_for_seg × otsu_seg_methods combination

File layout

Rule	Output
compute_spim_histogram	sub-*/seg/stain-*/level-*/histogram.npz
aggregate_histograms	group/stain-*/level-*/histogram.npz
multiotsu_from_batch_histogram	group/stain-*/level-*/desc-otsu+k{k}i{i}_thresholds.{png,tsv}
qc_batch_otsu_threshold_sweep	group/stain-*/desc-otsu+k{k}i{i}_batchotsuthreshqc.html

The per-subject qc_otsu_threshold_sweep and multiotsu rules are unchanged; the new batch pipeline is additive.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• zenodo.org
  • Triggering command: /usr/bin/python3 python3 ./spimquant/run.py /home/REDACTED/work/SPIMquant/SPIMquant/tests/bids_ds /tmp/test_out participant -np (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)