Notebook rework 1: one column, no inner scroll box, every channel in the quick scan; Compare groups in the run step

AGENTS.md

@@ -314,9 +314,21 @@ src/morphobricks_preprocessing/
                     (plan §12 Q26, Q31). Since PP-9 it holds the page methods, __init__ and
                     the shared helpers; the step methods live on mixin classes in the modules
                     below, and it re-exports every public name it had (`__all__`)
-  notebook_steps.py         steps(): the shipped notebook's 13 steps, one at a time (PR 17a; pure
-                            composition of the cards below); notebook_stepper.py the strip, Back/Next
-                            and the overview; notebook_step_states.py each step's done/one-line state
+  notebook_steps.py         steps(): the shipped notebook's 12 steps, one at a time (PR 17a; pure
+                            composition of the cards below); notebook_stepper.py the strip, Back/Next,
+                            the overview, the compact page (one screen per step: the cards scroll in
+                            their own box) and about()/field_rows(); notebook_step_states.py each
+                            step's done/one-line state
+  notebook_compact.py       the Images and Run steps arranged for one screen: one Folders card, the
+                            collapsed panels, and Compare groups (the former statistics page) in the
+                            run step (redesign of 10 November 2026)
+  notebook_progress.py      Wait: one line per wait (done of total, item, elapsed, time left once
+                            measurable); progress_html, time_left (pure parts)
+  notebook_quick_scan.py    the first step's quick scan: the folder walk only, one random image for
+                            looking only, then the explicit click that reads every header
+  axis_example.py           which planes the axes step's example shows (pure): one tile per channel,
+                            a few time points or slices; notebook_plots.example_png draws them
+  pixel_size_summary.py     the pixel size in one line, which images differ and where (pure)
   notebook_names.py         the names card's rows (conditions on step 4, replicates on step 5)
   notebook_axes_quick.py    the stepper's one-click Confirm these axes (Q3, PR 17b)
   notebook_row_fold.py      reopen: unchanged, answered rows fold; new or changed rows orange
@@ -747,9 +759,12 @@ Technical details go to `logging` (shown in the notebook's "Technical details" p
 | Masks (Q32) | Optional masks folder outside the experiment, one subfolder per mask type mirroring the experiment's folders, or the experiment's folders with `<image>_<type>.tif` (both may be mixed; `ambiguous_mask` when a name could fit two images or both layouts), paired by leaf folder + `position_id`; OME-Zarr label images are masks too. Header-only errors (`masks_folder_not_found`, `masks_inside_experiment`, `mask_names_differ_in_case`, `duplicate_mask`, `ambiguous_mask`, `unreadable_mask`, `mask_not_2d`, `mask_size_mismatch`, `mask_pixel_type`) and warnings (`mask_missing`, `mask_without_image`, `mask_outside_type_folder`) in `check`/`run`; manifest key `masks` (optional, version 1). Optional mask step (`masks` command, `scan_masks`): kinds, relations with evidence, direct-parent hierarchy, `mask_relationships.json` (report version 1); default thresholds the user may change (`thresholds=` keyword, one CLI option each, checked by `mask_thresholds`, written in the report); suggestions only, the user names and confirms. SciPy core dependency. Confirmed by the owner: 2D masks at the image's YX, integer/bool pixels, masks folder outside the experiment. Next: notebook step and a file of the user's answers; tag v0.2.0 proposed after merge. Plane identity (issue #36): masks may have Z and/or T named in their own metadata (never guessed: unnamed axes are `mask_not_2d`); the masks of an image share their planes (`mask_planes_differ`) and `run` checks them against the image's confirmed roles (`mask_planes_mismatch`, `mask_plane_issues`), so a 2D mask is refused for a Z-stack or time-lapse; manifest mask entries gain `axes` and `shape` (optional keys, version 1); `read_mask(z=, t=)` reads one plane; `scan_masks` scans plane by plane |
 | Notebook style | Follow the lab's NucleiSky and LabChronicle notebooks (see §7) |
 | Widget widths | **99%**, never 100% |
+| Waits | Every wait over about a second shows `notebook_progress.Wait`: done of total, the item, elapsed time, time left once measurable. Readers take a `progress` callback; no bare spinner (owner, 10 November 2026) |
+| Disabled actions | Every disabled button has a visible `notebook_render.blocked_line` beside it saying what blocks it; a tooltip alone is a hidden refusal (owner, 10 November 2026) |
+| One screen per step | The shipped notebook's steps fit 1366 x 768: one row of chips, explanations under *About this step*, details in collapsed panels, long lists scrolling in their own box (owner, 10 November 2026) |
 | Paths and filenames in widget HTML and notebook text | **`<b>…</b>` / `**…**`, never `<code>` or inline code** |
 | Things the user must confirm | **Large buttons** in a highlighted question box (`ConfirmToggle`), never small checkboxes |
-| Statistics step | "Step 4 · Calculate the statistics (optional)": clearly optional, writes nothing. A CSV chooser (Browse…) is prefilled with the table just computed, otherwise empty. Not calculated automatically |
+| Statistics step | **Shipped notebook since v0.5.1: the collapsed *Compare groups* panel of the run step, for that run's table; no table chooser, no second intensity check (owner, 10 November 2026). The page below remains for `results_step()` without `steps()`.** "Step 4 · Calculate the statistics (optional)": clearly optional, writes nothing. A CSV chooser (Browse…) is prefilled with the table just computed, otherwise empty. Not calculated automatically |
 
 ---
 

CHANGELOG.md

@@ -45,6 +45,47 @@ OME-XML description is parsed (which images are marked is unchanged; a malformed
 debug line without a traceback), and while the capture is attached the package's DEBUG records
 go to the "Technical details" panel only, with WARNING and above still reaching the root handlers.
 
+### Notebook redesign 4: one column, less on screen; Compare groups in the run step
+
+Owner test of v0.5.0 (10 November 2026), items (a) and (b), and the owner's test of the first
+redesign the same day, items (m) and (n): "simple and minimalistic"; no box that scrolls inside
+the page; always one column. Layout only: no answer, check, refusal, draft, description or run
+output changes.
+
+- **One column, and the page scrolls as a whole.** Nothing in a step scrolls on its own (no
+  fixed-height step body, no table or file list with its own scroll bar), and no cards, panels
+  or columns sit side by side. A step is short because it says less: its explanation is folded
+  under **About this step**, a card's help paragraph is one line that opens when pointed at,
+  details are collapsed panels, and cards, tiles, tables, buttons and pictures are denser. The
+  strip is one row; a step's title and purpose are one line.
+- **Images:** one *Folders* card with three labelled rows (images, masks, output); **Scan the
+  folders**, what it found, then **Looks right: read all image headers**, one under the other.
+  The scan shows the conditions in a short table (every folder under *All N folders*). After
+  the check the scan makes way for the result, and the pictures per folder, the check report
+  and *Exclude images* are collapsed panels.
+- **The quick scan shows every channel of its one image side by side** across the page, each
+  with its own contrast and its `c=` index, when that image's header names a channel axis
+  (`header_preview.header_channels`): up to six, and with seven or more it shows six and says
+  "6 of N channels shown". Display only, read from that one image; a header that names no
+  channel axis gets the one picture as before (no channel is guessed from the shape).
+- **Axes:** one row per dimension (what the file has, its role, what the role does), then the
+  example, then the pixel size, one under the other. A refusal of the roles is one sentence
+  with *Files and what to do* on demand (`notebook_render.issues_brief_html`), e.g. "Error ·
+  different channel counts: The images have different numbers of channels: 3 channels (10
+  images), 4 channels (4 images)."
+- **Run:** *Before you run* is shown only while something is missing; *Settings and mode* and
+  *What will happen* are collapsed; after a run the intensity checks and plots, **Compare
+  groups** and the report are collapsed panels.
+- **Compare groups replaces the optional statistics page** in the shipped notebook: the
+  grouping, the percentiles, the pooled statistics and the distribution plot of the table this
+  run wrote. There is no table to choose and the intensity checks are not repeated.
+  `results_step()` after `steps()` returns an empty hidden box, so the shipped notebook's cell
+  needs no change; called without `steps()` it is the page it was.
+- **`welcome()` is one line** (name, version, "the notebook is ready"); the *What next?* boxes
+  are not shown in the stepper.
+- The stacked pages other bricks embed (`folder_step`, `axis_step`) get the one-column axes
+  layout (roles, example, then the named-axis copies card); nothing else changes for them.
+
 ### Notebook redesign 3: the axes step shows the data as the roles read it; pixel size in one line
 
 Owner test of v0.5.0 (10 November 2026), items (e) and (f). The shipped notebook has 12 steps:

docs/colab-release-check.md

@@ -93,15 +93,16 @@ The notebook has three code cells, run in order: **1. Install MorphoBricks prepr
     Step 1 without running. The button is enabled, names the earlier run, and works.
 14. - [ ] Move the masks folder on Drive and click: a red card says the masks folder does not
     exist, and nothing is written.
-15. - [ ] The tables scroll inside the card, with no horizontal page scrollbar.
+15. - [ ] The page scrolls as a whole: no box inside it has its own scroll bar, and there is no
+      horizontal page scrollbar.
 
 ## E. Make named-axis copies (PR #127)
 
 16. - [ ] Run Step 0, then Step 1 on an experiment of Y/X-swapped OME-TIFFs on Drive, and
     press **Check folder**.
 17. - [ ] In Step 2, swap the Y and X roles. The red axis check appears, with the **Make
     named-axis copies (optional)** card under it. Its button is disabled.
-18. - [ ] Press **Show preview** and **Yes, the preview looks right**, then **Yes, write the
+18. - [ ] Look at the example (drawn by itself) and press **Yes, the example looks right**, then **Yes, write the
     copies with these roles**.
 19. - [ ] Press **Browse…**: the amber card names **Copy path**. Paste a Drive folder inside
     the experiment and check that it is refused. Then paste one next to the experiment.

docs/user_guide.md

@@ -265,6 +265,65 @@ notebook's step 3 (§4), also tells how they relate.
 
 ## 4. The notebook, step by step
 
+### The app in short (v0.5.1)
+
+Cell 3 opens the app: a strip of twelve steps, one on screen at a time, with **Back** and
+**Next** under it (**Next** is never blocked; a chip opens its step). The page is one column
+and scrolls as a whole: nothing scrolls inside its own box and nothing sits side by side.
+Explanations are folded under **About this step**, and details are in collapsed panels.
+Every wait shows a bar with what is done of the total, the file being read, the time elapsed
+and, once it can be measured, the time left. Every greyed-out button has a line beside it
+saying what it waits for.
+
+1. **Images.** Give the folders (images; masks and output are optional). **Scan the folders**
+   lists the conditions and folders with their image counts without reading any image header,
+   and shows one image chosen at random, with its path, for looking only: it is not used for
+   anything. Every channel of it is shown side by side (`c=0`, `c=1`, …, each with its own
+   contrast; at most six, and then it says *6 of N channels shown*).
+   If this is your experiment, click **Looks right: read all image headers**; the
+   headers are then read and checked. Changing a folder asks for a new scan. The pictures of
+   each folder, the check's report and **Exclude images** are collapsed below.
+2. **Axes.** One row per image dimension with its role, and under them an **example of one
+   image as these roles read it**: one tile per channel (`c=0`, `c=1`, …), a few time points
+   or slices, or the single plane, each with its height and width. It is drawn by itself and
+   redrawn whenever you change a role, so a wrong role looks wrong (a strip, stripes). Another
+   image or other planes are under **Another image, or other planes**. Nothing is confirmed
+   for you: click **Confirm these axes** (offered when the headers name every axis and
+   nothing is open), or **Yes, the example looks right** and then **Confirm axis roles**.
+   - **Pixel size** is one line here: for example *Pixel size: 0.108 × 0.108 µm (from the
+     headers, same in all 270 images)*. When the headers give none, type it once and click
+     **Use for all images** (or choose *pixels: deliberately uncalibrated*); leaving it empty
+     records the images as uncalibrated, nothing is guessed. When the headers do not agree,
+     the line says how many images have which size and in which folders, and **Set per
+     imaging unit…** opens: there you state a size for one folder (imaging unit) or image.
+     **Use for all images** is your statement for every image: it replaces sizes stated per
+     folder, and a size that differs from an image's header is still listed as a warning.
+3. **Conditions**, 4. **Replicates**, 5. **Compared against**, 6. **Image type**, 7. **Stains**,
+   8. **Tag channels**, 9. **Masks**: one kind of answer per step, saved as you give it.
+10. **Check and save.** Your experiment in sentences, one question per replicate, then **Yes,
+    save the experiment description**. The line beside the button says what is still missing.
+11. **Run.** **Compute histograms**; what is still to do is listed only while something is.
+    The settings and *What will happen* are collapsed. After the run: its result, and collapsed
+    panels for the **intensity checks and plots**, **Compare groups** and the report.
+    **Compare groups** replaces the former optional statistics page: choose how to group
+    (condition, biological repeat, technical repeat or image) and click **Calculate
+    statistics** for the pooled statistics and the distribution plot of the table this run
+    wrote. It writes nothing.
+12. **Describe the masks** (optional), after a run that recorded masks.
+
+Images with different numbers of channels (for example three in most folders and four in
+one) are refused in this version (`different_channel_counts`): the axes step names the error in
+one sentence, with the files and what to do one click away, and **Confirm axis roles** says
+that this is what it waits for.
+
+The rest of this section describes each card in detail. It is written for the same cards
+shown as stacked pages (as other bricks embed them); where the app differs, the list above
+is what you see. In particular: **Show preview** and **Yes, the preview looks right** are the
+example and **Yes, the example looks right**; **Check folder** is **Looks right: read all
+image headers**; and step 4 below is the **Compare groups** panel.
+
+### The cards in detail
+
 The notebook's code cells are hidden: run them from top to bottom (click a cell and press
 **Shift + Enter**). Each step is a page of boxes. A blue box at the top says what the step
 is for, every control has a grey help line, and one coloured message says what happened

notebooks/MorphoBricks_Preprocessing.ipynb

@@ -14,7 +14,7 @@
     "- **Confirms the experimental design**: folder labels, biological-repeat pairing and controls.\n",
     "- **Confirms image interpretation**: axis roles and fluorescence/RGB image type. Scientific metadata are never silently guessed.\n",
     "- **Computes per-plane intensity histograms** used by downstream MorphoBricks.\n",
-    "- **Runs intensity QC** and provides optional pooled statistics after preprocessing.\n",
+    "- **Runs intensity QC** and, on request, compares groups after preprocessing.\n",
     "\n",
     "### Before you start\n",
     "\n",
@@ -372,12 +372,12 @@
     "\n",
     "In the app:\n",
     "\n",
-    "1. Give the **experiment folder** and optional **output/masks folders**, then click **Check folder**.\n",
-    "2. Go through the steps one at a time with **Next** (or click a step in the strip at the top): axes, pixel sizes, conditions, replicates, comparisons, image type, stains, channel tags and masks.\n",
+    "1. Give the **experiment folder** (masks and output folders are optional) and click **Scan the folders**. Look at the folders and the example image, then click **Looks right: read all image headers**.\n",
+    "2. Go through the steps one at a time with **Next** (or click a step in the strip at the top): axes and pixel size, conditions, replicates, comparisons, image type, stains, channel tags and masks.\n",
     "3. On **Check and save**, read your experiment in words and save it; then **Run** computes the histograms.\n",
-    "4. Review the QC results; pooled statistics are optional.\n",
+    "4. After the run, the intensity checks and **Compare groups** are collapsed panels of the run step.\n",
     "\n",
-    "Detailed explanations appear inside the app only where a decision is required."
+    "Every wait shows its progress, and a greyed-out button says beside it what it waits for."
    ]
   },
   {

pyproject.toml

@@ -142,6 +142,7 @@ baseline = "tools/code_rules_baseline.json"
 "morphobricks_preprocessing.run_labels" = "io"
 "morphobricks_preprocessing.notebook_axes" = "ui"
 "morphobricks_preprocessing.notebook_progress" = "ui"
+"morphobricks_preprocessing.notebook_compact" = "ui"
 "morphobricks_preprocessing.notebook_quick_scan" = "ui"
 "morphobricks_preprocessing.notebook_axes_quick" = "ui"
 "morphobricks_preprocessing.notebook_channel_thumbs" = "ui"