v0.7.0 - output naming refactor, vessels, mri preproc, and more

What's Changed

• fix for merging tsvs by @akhanf in #95
• Fixes for --register-to-mri workflow by @Dhananjhay in #94
• upgrade zarrnii, add --no-segmentation option by @akhanf in #96
• Set up MkDocs documentation structure with Material theme by @Copilot in #102
• Add inline docstrings to workflow modules for automated documentation by @Copilot in #104
• Add modular Mermaid workflow DAG diagrams with regeneration script by @Copilot in #103
• Add native mermaid diagram support to MkDocs documentation by @Copilot in #106
• Add HTML QC reports for MRI to SPIM registration by @Copilot in #105
• New features for --register-to-mri option by @akhanf in #107
• Add auto-generated argparse CLI documentation to mkdocs by @Copilot in #110
• upgrade zarrnii for units fix by @akhanf in #111
• Add multi-MRI preprocessing with rigid registration and averaging by @Copilot in #109
• Add How-To Guides section to mkdocs.yml navigation by @Copilot in #113
• WIP: Revisions to documentation by @akhanf in #108
• Zarrnii plugins by @akhanf in #118
• Fix stain-for-reg fallback when spim_templates exists but has no matching stains by @Copilot in #115
• accommodate new templates from SPIMtemplates workflow by @akhanf in #112
• Pass orientation override to vessel segmentation via zarrnii_kwargs by @Copilot in #122
• Make signed distance transform physically calibrated and handle homogeneous blocks by @Copilot in #121
• Add signed distance transform rule and script by @Copilot in #120
• Vessel segmentation by @akhanf in #119
• Add mask-based colocalization analysis via signed distance transform by @Copilot in #123
• Expose dask scheduler to CLI and unify across all workflow scripts by @Copilot in #125
• Performance updates by @akhanf in #126
• Refactor segmentation and vessels workflows by @akhanf in #130
• fix units for ds test data by @akhanf in #133
• Add concatenated composite transforms for SPIM↔template and MRI↔SPIM by @Copilot in #132
• Aba lvl atlases by @amrka in #114
• Bump the dependencies group with 2 updates by @dependabot[bot] in #73
• Update zarrnii by @akhanf in #137
• large naming refactor by @akhanf in #138
• docs: update output directory structure to reflect naming refactor by @Copilot in #139
• [Docs] Overview of SPIMquant Workflows and Output Types by @Copilot in #140
• Add subject-level visual QC outputs (histogram, segmentation, z-profile, object stats, ROI summaries, vessel overlays) by @Copilot in #141
• resource updates for coloc run by @akhanf in #143
• feat: improve zoom montage QC PNGs — better mask color, no-mask output, n4 bg option by @Copilot in #144
• Add animated GIF QC for per-instance and coloc crops by @Copilot in #145
• Replace fixed histogram range/bins in multiotsu with percentile-based range and bin-width; add threshold sweep QC report by @Copilot in #146
• Remove k wildcard from Atropos segmentation, add automatic k-retry logic by @Copilot in #151
• fix for stains list by @akhanf in #153

New Contributors

• @amrka made their first contribution in #114

Full Changelog: v0.5.0-alpha1...v0.7.0

v0.5.0-alpha1 - co-localization analysis & group stats

What's Changed

• Add regionprops coordinate transformation to template space with stain aggregation by @Copilot in #76
• Add KDTree-based colocalization analysis for multi-channel regionprops by @Copilot in #77
• add coloc atlas heatmaps by @akhanf in #80
• Add group-level statistical analysis with contrast-based comparisons by @Copilot in #78
• refactoring and fixes to tsv and group stats by @akhanf in #81
• Add subject-level parquet concatenation rules for aggregate instance analysis by @Copilot in #82
• Make heatmap height scale proportionally with number of atlas regions by @Copilot in #84
• Add contrast filtering to group-level parquet processing rules by @Copilot in #83
• Add colocalization visualization notebook with explanatory figures by @Copilot in #85
• update figures for presentation by @akhanf in #86
• fix fig in example notebook by @akhanf in #87
• Add create_imaris_crops rule for high-resolution atlas region extraction by @Copilot in #79
• Add registration QC report generation with HTML output and nilearn visualizations by @Copilot in #88
• Add group-averaged segstats maps to template space by contrast by @Copilot in #89
• bump zarrnii to 0.14.1 by @akhanf in #91
• Replace equality comparison with identity comparison for None checks by @Copilot in #93
• clean up target rules, check stains for all subjects by @akhanf in #92

Full Changelog: v0.4.0-alpha1...v0.5.0-alpha1

v0.4.0-alpha1

What's Changed

• Marm fixes by @akhanf in #51
• Add dsurqe template by @akhanf in #50
• fix for nii/nii.gz compatibility by @akhanf in #54
• Add module-level docstring to map_atlas_to_centroids.py by @Copilot in #56
• Add module-level docstring to compute_centroids.py by @Copilot in #57
• Add module-level docstring to clean_segmentation.py by @Copilot in #58
• Add module-level docstring to merge_into_segstats_tsv.py by @Copilot in #59
• Segmentation cleaning and computing centroids by @akhanf in #55
• Bump prefix-dev/setup-pixi from 0.9.1 to 0.9.2 in the dependencies group by @dependabot[bot] in #52
• bump version of zarrnii to fix bug by @akhanf in #60
• specify agg matplotlib backend by @akhanf in #61
• Add wet run testing logic by @Dhananjhay in #53
• Add work directory option for intermediate zarr storage by @Copilot in #62
• Add resource specifications (threads, mem_mb, runtime) to all Snakemake rules by @Copilot in #63
• Parquet centroids & counts nifti by @akhanf in #64
• Add temp() directive and disk_mb resource to zarr output rules by @Copilot in #66
• Add group directive to subject-specific rules for node-local storage by @Copilot in #65
• Add snakemake rules for creating patches from zarr data by @Copilot in #67
• Save final ome zarrs as ozx by @akhanf in #68
• Add --patch_atlas_segs CLI argument for patch extraction by @Copilot in #69
• Refactor level & other dag improvements by @akhanf in #70
• Fix n4 by @akhanf in #72
• updates to use latest zarrnii regionprops integration by @akhanf in #71
• Custom regionprop filter per stain/channel by @akhanf in #74

Full Changelog: v0.3.0-alpha1...v0.4.0-alpha1

v0.3.0-alpha1

What's Changed

• fix relpath issue with bids_dir by @akhanf in #48
• use new zarrnii atlas functions by @akhanf in #46
• Fix issues with segmentation /fieldfrac by @akhanf in #49

Full Changelog: v0.2.1-alpha1...v0.3.0-alpha1

v0.2.1-alpha1

What's Changed

• Orientation patch by @akhanf in #47

Full Changelog: v0.2.0-alpha1...v0.2.1-alpha1

v0.2.0-alpha1

What's Changed

• Improve SPIMquant directory structure by @Karl5766 in #14
• Stains from ome-zarr, and Eed atlas labels by @akhanf in #16
• threshold-based segmentation, coiled for N4/thresholding, BIDS app CLI, gubra and marmoset template, by @akhanf in #18
• Various fixes to clean-up CLI, and get segmentation working on local compute (without coiled) by @akhanf in #19
• add gubra files (download tar), other cleanup by @akhanf in #20
• Turone by @akhanf in #21
• add missing upath dependency by @akhanf in #22
• change default work path by @akhanf in #23
• utils fix by @akhanf in #25
• another fix for cloud storage uris by @akhanf in #26
• couple more pesky fixes for storage creds by @akhanf in #27
• initial version of lightsheet-mri intra-subject registration by @akhanf in #28
• add Ngo atlas to ABAv3 template by @akhanf in #29
• Pixi refactor, zarrnii 0.3.0 (uses zarr v3), remove containers by @akhanf in #31
• updates and fixes for segmentation workflows by @akhanf in #30
• Pipeline cleanup by @Dhananjhay in #32
• fixes for zarr with no z downsampling by @akhanf in #33
• use temp() on more files by @akhanf in #34
• Add --template-crop CLI option for hemisphere-specific template registration by @Copilot in #36
• add downsampled dataset by @akhanf in #37
• Clean up extraneous rules, scripts, notebooks, and config parameters not used in default workflow by @Copilot in #38
• Refactor for updates to zarrnii, plugins etc by @akhanf in #39
• Bump the dependencies group with 2 updates by @dependabot[bot] in #40
• Update documentation to use pixi instead of pip and singularity for installation by @Copilot in #42
• Add GitHub Copilot instructions for SPIMquant development by @Copilot in #43

New Contributors

• @Karl5766 made their first contribution in #14
• @Dhananjhay made their first contribution in #32
• @Copilot made their first contribution in #36
• @dependabot[bot] made their first contribution in #40

Full Changelog: v0.1.0-alpha2...v0.2.0-alpha1

v0.1.0-alpha2

What's Changed

• bugfix: was passing channel index for nifti by @akhanf in #9
• bugfix: console script for spimquant cli had a typo by @akhanf in #10

Full Changelog: v0.1.0-alpha...v0.1.0-alpha2

Initial alpha release

What's Changed

• update to use latest snakebids 0.12.0 run.py by @akhanf in #1
• Several new features added, and refactoring.. by @akhanf in #2
• updates to deps, warp to template without zooms by @akhanf in #3
• Reduce runtime for warping to template, by initial downsampling by @akhanf in #5
• Docs updates by @akhanf in #4
• bump up to latest release of zarrnii by @akhanf in #7

New Contributors

• @akhanf made their first contribution in #1

Full Changelog: https://github.com/khanlab/SPIMquant/commits/v0.1.0-alpha