v0.5.2

What's Changed

• Fixes #258, fixes #252 by @guijacquemet in #278
• Fixes #279 by @guijacquemet in #280
• Fixes #281 by @guijacquemet in #282
• Stage 3 S3.3: per-unit channel lists, plane_histograms v5 by @guijacquemet in #288
• Parent-label (grouped) masks: re-pin Spec 69a58b3, resolver contract v2 by @guijacquemet in #289
• Notebook: one image viewer for every step, formatted report, X/Y pixel inputs (redesign 3, part 1) by @guijacquemet in #284
• Notebook: axes proposed at the quick scan and validated on all images; pixel sizes that differ in one line (redesign 3, part 2) by @guijacquemet in #285
• Notebook: Z-stacks saved as recorded projections from the Axes step; 3-D stacks kept recorded (redesign 3, part 3) by @guijacquemet in #286
• OME-Zarr copies: asked on the first screen, written as a recorded conversion once the axes are confirmed (redesign 3, part 4) by @guijacquemet in #287
• Conversion record version 4: refuse version 3, require source_relative_path where written by @guijacquemet in #291
• Axes: show the confirmation at once and make it faster; image type moves to Channels (v0.5.2 owner feedback) by @guijacquemet in #292
• Release v0.5.2 by @guijacquemet in #290

Full Changelog: v0.5.1...v0.5.2

v0.5.1

What's Changed

• PP-C1: drop the v0.4.0 parity tests, keep the histogram goldens (v0.5.1, 1/3) by @guijacquemet in #259
• PP-C2: every run is described; undescribed runs and their compatibility code removed (v0.5.1, 2/3) by @guijacquemet in #260
• PP-C3: document that every run is described (v0.5.1, 3/3) by @guijacquemet in #261
• RunInputs.resolve_request: the shared request resolver (contract v1, v0.5.1) by @guijacquemet in #256
• PP-1: Fov.image_type per position, partial-mask helper, pinned brick surface by @guijacquemet in #263
• PP-2: lab-tool links (--lab-links), recorded in the run manifest only by @guijacquemet in #264
• SWEEP-PP (A): remove the remaining compatibility code (PP-05..PP-10) and fix the frozen clock (#262) by @guijacquemet in #265
• SWEEP-PP (B): experiment_design.csv is output only, and the pairing card is rebuilt on the draft (PP-02) by @guijacquemet in #266
• Notebook: three code cells (1. Install, 2. Mount Google Drive, 3. Run preprocessing) by @guijacquemet in #267
• Pin morphobricks-normalization v0.4.0 (position_id required) by @guijacquemet in #268
• Quiet the notebook output: no debug flood from ImageJ TIFFs by @guijacquemet in #271
• Notebook redesign 1: file lists without empty bullets, the references dropdown stays, disabled actions say why by @guijacquemet in #269
• Notebook redesign 2: progress for every wait, progress callbacks from the readers, quick scan first by @guijacquemet in #270
• Notebook redesign 3: the axes step shows the data as the roles read it; pixel size in one line by @guijacquemet in #272
• Drop the legacy experiment_design.csv migration (PP-03) by @guijacquemet in #274
• Notebook rework 1: one column, no inner scroll box, every channel in the quick scan; Compare groups in the run step by @guijacquemet in #275
• Notebook rework 2: seven steps (Images, Axes, Channels, Masks, Design, Check and save, Run) by @guijacquemet in #276
• Release v0.5.1 by @guijacquemet in #277

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

• [after-v0.4.0-tag] Roadmap: explicit projection step (P1) and experiment schema (P2) by @guijacquemet in #174
• I/O minors: same_file export, OME-Zarr time unit, open errors, 1-D refusal by @guijacquemet in #177
• Per-channel group statistics and explicit refusal of cyclic mask hierarchies by @guijacquemet in #178
• Bind masks to their fingerprints for the whole run and the relationship scan by @guijacquemet in #180
• Index MaskInventory by image once (for_image O(1)) by @guijacquemet in #181
• Doc cleanup: archive plan milestones and status log, refresh v0.4.0 status by @guijacquemet in #182
• Vendor the Spec conformance fixtures at a pinned commit (Stage 1, PR 1 of 3) by @guijacquemet in #183
• Strict description reader, phases 1-3 (Stage 1, PR 2 of 3) by @guijacquemet in #184
• Strict description reader, phases 4-5 and warnings (Stage 1, PR 3 of 3) by @guijacquemet in #185
• Re-pin the vendored Spec to 745259b; condition single rule (Stage 1, PR A) by @guijacquemet in #186
• Description model, canonical writer and section digests (Stage 1, PR 4) by @guijacquemet in #187
• Description publication: lock, base SHA, symlink refusal, transitions, records (Stage 1, PR 5) by @guijacquemet in #188
• Turn content hashing of the sources on by default by @guijacquemet in #189
• Discovery and header additions for the experiment description (Stage 1, PR 6) by @guijacquemet in #190
• Reconciliation of the published description with the folder (Stage 1, PR 9) by @guijacquemet in #193
• Physical R_* checks of an experiment description (Stage 1, PR 8) by @guijacquemet in #192
• Safe display of planes: reduced reads, channel strip, mask overlay (Stage 1, PR 13) by @guijacquemet in #194
• Draft description, proposed IDs and legacy design migration (Stage 1, PR 7) by @guijacquemet in #191
• Re-pin the vendored Spec to 7dbae0c (byte rules, goldens, t13, records encoding) by @guijacquemet in #195
• Say a time step cannot be stated in calibration.csv by @guijacquemet in #201
• Derived experiment_design.csv and cross-version parity suite (Stage 1, PR 10) by @guijacquemet in #196
• Detect mask hierarchy cycles before reducing direct edges by @guijacquemet in #200
• Re-check every mask fingerprint right before the manifest replacement by @guijacquemet in #202
• Hold module-level skips and missing modules in the Spec test gate by @guijacquemet in #205
• Make the records append rollback-safe and validate record shapes by @guijacquemet in #207
• Re-pin the vendored Spec to b197ac1; reserved names apply to used_ids.channels by @guijacquemet in #208
• Run integration of the published experiment description (Stage 1, PR 11) by @guijacquemet in #209
• Semantic RunInputs from a published description (Stage 1, PR 12) by @guijacquemet in #210
• Notebook bootstrap: show the Git identity of a local checkout and refuse a non-release one by @guijacquemet in #214
• Z projection 1/6: the pure arithmetic (part of #176) by @guijacquemet in #211
• Z projection 2/6: conversion record version 3 (part of #176) by @guijacquemet in #212
• Spec conformance P26: per-unit header channel-name checks for described runs by @guijacquemet in #218
• Description reader: own rule vocabulary; pin path and value of five refusals by @guijacquemet in #219
• CLI describe, docs and conformance run (Stage 1, PR 17) by @guijacquemet in #220
• Draft file and draft-to-description (Stage 1) by @guijacquemet in #221
• Z projection 3/6: plan and write projected copies (part of #176) by @guijacquemet in #213
• Z projection 4/6: convert --project on the command line (part of #176) by @guijacquemet in #215
• Publication writes the removed and image_count_changed records (RR2, RR1) by @guijacquemet in #216
• Refuse a draft written under another Spec commit at resume and save by @guijacquemet in #224
• List images without header channel names in a described run by @guijacquemet in #226
• Stage 2: described runs write manifest version "4" by @guijacquemet in #227
• Stage 2: make_clean_run(description=...) builds a described run for tests by @guijacquemet in #228
• Stage 2: A_* error classes and RunInputs.section_digests() by @guijacquemet in #229
• Z projection 5/6: the run side (part of #176) by @guijacquemet in #217
• Re-pin the vendored Spec to c8f6852 by @guijacquemet in #230
• Notebook Step 1 cards: IDs, names, pairing, references (Stage 1, PR 14) by @guijacquemet in #231
• Document the window after the final mask check by @guijacquemet in #232
• Notebook: your channels (labels first, then tag per unit) (Stage 1, PR 15) by @guijacquemet in #233
• Fixes #234: make_described_run spreads image_count over technical repeats by @guijacquemet in #236
• Notebook: your masks (Stage 1, PR 16a) by @guijacquemet in #237
• Notebook: check and save, reopen (Stage 1, PR 16b) by @guijacquemet in #238
• Run page: channel and replicate IDs, no-problems icon, plan card, mask kinds by @guijacquemet in #241
• Re-pin Spec 1bed024; read_records follows §4.6 (R_RECORDS_FILE_INVALID) by @guijacquemet in #242
• Described runs: pixel-type and dimension checks per unit (#239, narrowed) by @guijacquemet in #243
• Notebook: one step at a time, in the decided order (PR 17a) by @guijacquemet in #244
• Report the layout refusal first in described runs with several layouts by @guijacquemet in #246
• Notebook: tags per header block, colour pictures, one-click axes (PR 17b-1) by @guijacquemet in #247
• Notebook: fold unchanged rows on reopen (PR 17b-2) by @guijacquemet in #248
• Notebook: Stains is not applicable when every folder is colour (RGB) by @guijacquemet in #249
• Notebook: folder pictures with a 1:1 crop, tag like the saved group, colour mask evidence (PR 17c) by @guijacquemet in #250
• Audit batches 33, 34a, 34b: publish only what was answered, of the image checked by @guijacquemet in #254
• Batch 34b: preview-gat...

v0.4.0

What's Changed

• Keep an unreadable experiment_design.csv untouched in step 1 by @guijacquemet in #61
• load_design raises DesignCheckError for an unreadable experiment_design.csv by @guijacquemet in #62
• Read masks one pixel high or wide as 2D YX masks by @guijacquemet in #63
• PP-1: the axis check (swaps and contradictions are errors; plain stacks confirmed) by @guijacquemet in #64
• PP-0: code standards with a shrink-only baseline; one atomic writer, one grammar helper by @guijacquemet in #65
• PP-2: remove convert_tiffs, zarr_export, the moved-name shims and the old axis functions by @guijacquemet in #66
• PP-3: split run.py into the run package (move only) by @guijacquemet in #109
• PP-4: manifest version 2, row keys, per-file plain-stack confirmation by @guijacquemet in #110
• PP-5: masks (stated axes, never converted, labels always used) by @guijacquemet in #111
• PP-6: RunInputs and testing.make_clean_run by @guijacquemet in #112
• PP-7: modes, lock and report by @guijacquemet in #113
• PP-8: calibration (stated pixel sizes, recorded with their source) by @guijacquemet in #114
• Roadmap: quick quality checks from whole-FOV embeddings and masks by @guijacquemet in #116
• PP-8b: refuse X-before-Y masks in the run; RunInputs names unrecorded files by @guijacquemet in #115
• PP-8c: fixes from running on real data (file modes, absent-axis sizes, masks inputs, stopped-run text, read arguments, design command) by @guijacquemet in #117
• PP-8d: Colab and LabConstrictor readiness of the notebook by @guijacquemet in #118
• PP-9: split notebook_ui.py (move only) and pin the embedding API by @guijacquemet in #119
• PP-10a: notebook cards (calibration, design, recorded inputs, report, stale lock) by @guijacquemet in #120
• PP-10b: notebook debt from PP-9 (computation out of the UI, functions within §9) by @guijacquemet in #121
• PP-10c: the notebook's masks field and mask-axis statements by @guijacquemet in #122
• PP-10d: the notebook's masks-step button (Describe the masks) by @guijacquemet in #123
• Release v0.4.0rc3: version and the notebook's pinned tag by @guijacquemet in #125
• PP-11: convert, named-axis OME-TIFF copies of images with axis errors by @guijacquemet in #124
• PP-11c: conversion integrity (copy SHA-256, metadata epochs, exact CLI sizes) by @guijacquemet in #126
• PP-11b: the notebook's Make named-axis copies card by @guijacquemet in #127
• OME-Zarr axes and calibration: nothing guessed, nothing silent (#72, #73, #94) by @guijacquemet in #129
• Experiment design identity and counts: excluded folders, duplicate columns, output folder (#82, #83, #98) by @guijacquemet in #130
• Links stay inside the experiment and masks folders; --log is checked before it opens (#81, #99) by @guijacquemet in #128
• Micrometre conversions are always positive and finite; check and design exit 1 on errors (#93) by @guijacquemet in #133
• same_objects is a one-to-one matching; size and plane-count warnings follow the confirmed roles (#67, #74) by @guijacquemet in #131
• PP-12: staging and resume, crash-consistent publication, OME-Zarr inventory fingerprint (#86, #90) by @guijacquemet in #132
• PP-13: migration guide, CHANGELOG, Colab release check, docs pass; version 0.4.0rc4 by @guijacquemet in #134
• Audit B1, I1: keep the experiment, copies and output out of the masks folder by @guijacquemet in #135
• Audit I4: notebook inputs start from the earlier run's recorded inputs by @guijacquemet in #137
• Fix audit findings I2, I3, I5, m4, m5, m6 (what RunInputs gives the bricks) by @guijacquemet in #136
• Compare output and copy folders with the experiment by device and inode by @guijacquemet in #138
• Fix cross-brick test findings F1, F8, F9, F10, F11 by @guijacquemet in #139
• Fix the rc4 external review: mount points, hard links, commit fsync, content verification by @guijacquemet in #140
• Round-2 audit fixes: strict v2 position_id (A-m5), physical-size read errors (A-m6), exact unit conversion (B-m7) by @guijacquemet in #142
• v0.4.0rc5: tie-break gives no parent, ImageJ unit without resolution, plan Q66/Q73/Q74, changelog by @guijacquemet in #143
• Pin normalization v0.3.3; warn about channels without finite pixels (normalization#57) by @guijacquemet in #145
• rc5 release blockers: strict manifest version 3, final content check before commit by @guijacquemet in #146
• Final v0.4.0 prep: shared write-target rule, normalization compatibility, #146 follow-ups by @guijacquemet in #147
• F10: check --missing-as-singleton; a YX-named 2-D mask is shared by a Z/T image by @guijacquemet in #148
• Commit a publication only once its manifest has left .publish by @guijacquemet in #149
• Share a 2-D mask across Z/T planes only when its type is stated YX by @guijacquemet in #150
• docs: add Colab notebook badge by @guijacquemet with @Copilot in #161
• Fix Colab widgets and simplify preprocessing notebook by @guijacquemet in #162
• Repair Colab/Jupyter notebook packaging and restore readable guidance by @guijacquemet in #163
• 2-D planes only: refuse Z-stacks, remove the stated shared 2-D mask (tracker row 36) by @guijacquemet in #173
• Release v0.4.0 by @guijacquemet in #175

New Contributors

• @guijacquemet with @Copilot made their first contribution in #161

Full Changelog: v0.3.4...v0.4.0

v0.4.0rc5

What's Changed

• Fix cross-brick test findings F1, F8, F9, F10, F11 by @guijacquemet in #139
• Fix the rc4 external review: mount points, hard links, commit fsync, content verification by @guijacquemet in #140
• Round-2 audit fixes: strict v2 position_id (A-m5), physical-size read errors (A-m6), exact unit conversion (B-m7) by @guijacquemet in #142
• v0.4.0rc5: tie-break gives no parent, ImageJ unit without resolution, plan Q66/Q73/Q74, changelog by @guijacquemet in #143
• Pin normalization v0.3.3; warn about channels without finite pixels (normalization#57) by @guijacquemet in #145
• rc5 release blockers: strict manifest version 3, final content check before commit by @guijacquemet in #146

Full Changelog: v0.4.0rc4...v0.4.0rc5

v0.4.0rc4

What's Changed

• PP-11: convert, named-axis OME-TIFF copies of images with axis errors by @guijacquemet in #124
• PP-11c: conversion integrity (copy SHA-256, metadata epochs, exact CLI sizes) by @guijacquemet in #126
• PP-11b: the notebook's Make named-axis copies card by @guijacquemet in #127
• OME-Zarr axes and calibration: nothing guessed, nothing silent (#72, #73, #94) by @guijacquemet in #129
• Experiment design identity and counts: excluded folders, duplicate columns, output folder (#82, #83, #98) by @guijacquemet in #130
• Links stay inside the experiment and masks folders; --log is checked before it opens (#81, #99) by @guijacquemet in #128
• Micrometre conversions are always positive and finite; check and design exit 1 on errors (#93) by @guijacquemet in #133
• same_objects is a one-to-one matching; size and plane-count warnings follow the confirmed roles (#67, #74) by @guijacquemet in #131
• PP-12: staging and resume, crash-consistent publication, OME-Zarr inventory fingerprint (#86, #90) by @guijacquemet in #132
• PP-13: migration guide, CHANGELOG, Colab release check, docs pass; version 0.4.0rc4 by @guijacquemet in #134
• Audit B1, I1: keep the experiment, copies and output out of the masks folder by @guijacquemet in #135
• Audit I4: notebook inputs start from the earlier run's recorded inputs by @guijacquemet in #137
• Fix audit findings I2, I3, I5, m4, m5, m6 (what RunInputs gives the bricks) by @guijacquemet in #136
• Compare output and copy folders with the experiment by device and inode by @guijacquemet in #138

Full Changelog: v0.4.0rc3...v0.4.0rc4

v0.4.0rc3

What's Changed

• PP-9: split notebook_ui.py (move only) and pin the embedding API by @guijacquemet in #119
• PP-10a: notebook cards (calibration, design, recorded inputs, report, stale lock) by @guijacquemet in #120
• PP-10b: notebook debt from PP-9 (computation out of the UI, functions within §9) by @guijacquemet in #121
• PP-10c: the notebook's masks field and mask-axis statements by @guijacquemet in #122
• PP-10d: the notebook's masks-step button (Describe the masks) by @guijacquemet in #123
• Release v0.4.0rc3: version and the notebook's pinned tag by @guijacquemet in #125

Full Changelog: v0.4.0rc2...v0.4.0rc3

v0.4.0rc2

What's Changed

• PP-7: modes, lock and report by @guijacquemet in #113
• PP-8: calibration (stated pixel sizes, recorded with their source) by @guijacquemet in #114
• Roadmap: quick quality checks from whole-FOV embeddings and masks by @guijacquemet in #116
• PP-8b: refuse X-before-Y masks in the run; RunInputs names unrecorded files by @guijacquemet in #115
• PP-8c: fixes from running on real data (file modes, absent-axis sizes, masks inputs, stopped-run text, read arguments, design command) by @guijacquemet in #117
• PP-8d: Colab and LabConstrictor readiness of the notebook by @guijacquemet in #118

Full Changelog: v0.4.0rc1...v0.4.0rc2

v0.4.0rc1

What's Changed

• Keep an unreadable experiment_design.csv untouched in step 1 by @guijacquemet in #61
• load_design raises DesignCheckError for an unreadable experiment_design.csv by @guijacquemet in #62
• Read masks one pixel high or wide as 2D YX masks by @guijacquemet in #63
• PP-1: the axis check (swaps and contradictions are errors; plain stacks confirmed) by @guijacquemet in #64
• PP-0: code standards with a shrink-only baseline; one atomic writer, one grammar helper by @guijacquemet in #65
• PP-2: remove convert_tiffs, zarr_export, the moved-name shims and the old axis functions by @guijacquemet in #66
• PP-3: split run.py into the run package (move only) by @guijacquemet in #109
• PP-4: manifest version 2, row keys, per-file plain-stack confirmation by @guijacquemet in #110
• PP-5: masks (stated axes, never converted, labels always used) by @guijacquemet in #111
• PP-6: RunInputs and testing.make_clean_run by @guijacquemet in #112

Full Changelog: v0.3.4...v0.4.0rc1

v0.3.4

• A plain stack declared YXC is accepted (positional Y/X no longer count as named axes).
• A declaration that differs from the header only by swapping Y and X is accepted and read transposed (declared_axes_transposed); any other disagreement is refused.
• New shared reader read_confirmed_design. Edits to the design file are refused, naming the row and column, when a repeat group is empty, NA-like or differs from another only by case, or when confirmed_on is not an ISO date (YYYY-MM-DD).