[Docs] Overview of SPIMquant Workflows and Output Types#140
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…on how-to Agent-Logs-Url: https://github.com/khanlab/SPIMquant/sessions/d5b8bdc3-a6bb-424a-908c-aaa90ca30549 Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
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[WIP] Add documentation overview for SPIMquant workflows and output types
[Docs] Overview of SPIMquant Workflows and Output Types
Mar 31, 2026
akhanf
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Mar 31, 2026
docs/howto/segmentation.md
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| A two-step unsupervised method that adapts to the intensity distribution of each image: | ||
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| 1. **Multi-Otsu thresholding** — Otsu's method is extended to find *N* thresholds that minimise within-class variance, splitting the histogram into background, low-signal, and high-signal classes. | ||
| 2. **k-means refinement** — 3-class k-means clustering (`k=3`) is applied to the voxels that fall in the intermediate class identified by Otsu, further separating ambiguous voxels. The result assigned class index `i=2` (the highest-intensity class) is kept as positive. |
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@copilot: it is not actually using k-means, it is simply a way to select which how many classes to use for multiotsu, and which of the levels to use for the binary classification. fix this
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Fixed in b191746. The description now correctly explains that k is the number of Otsu classes (with k-1 thresholds computed) and i is the 1-based index of the threshold to use for the binary classification — no k-means involved.
docs/workflow_overview.md
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| | Path pattern | Content | Stage | | ||
| |---|---|---| | ||
| | `sub-*/micr/*_space-{tpl}_SPIM.nii.gz` | Subject brain warped to template | 6 | | ||
| | `sub-*/micr/*_regqc.html` | Registration QC report | 10 | |
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| | `sub-*/micr/*_regqc.html` | Registration QC report | 10 | | |
| | `sub-*/xfm/*_regqc.html` | Registration QC report | 10 | |
Agent-Logs-Url: https://github.com/khanlab/SPIMquant/sessions/8c18a135-2cee-4627-a6fc-0c70d8b49319 Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
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approved these changes
Mar 31, 2026
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Adds the three documentation artifacts requested by the epic: a pipeline narrative, a complete output reference, and an enhanced segmentation how-to. Navigation is updated to surface all three.
New:
docs/workflow_overview.md— "How SPIMquant Works Under the Hood"sub-*/xfm/*_regqc.htmlfor registration QC reports)Rewritten:
docs/reference/outputs.mdtests/bids_dsRewritten:
docs/howto/segmentation.mdthreshold(fixed value) vsotsu+k3i2(adaptive multi-Otsu) with accurate description of thek(number of Otsu classes) andi(threshold index for binary classification) parameters, trade-offs, and per-stain YAML exampleNavigation (
mkdocs.yml,docs/index.md)