driftlessmap 1.5.0__tar.gz → 1.6.1__tar.gz

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/CITATION.cff

@@ -4,8 +4,8 @@ message: >-
   HERBS paper listed under references.
 title: DriftlessMap
 type: software
-version: 1.5.0
-date-released: 2026-09-27
+version: 1.6.1
+date-released: 2026-09-28
 authors:
   - name: Mohebi & Associates
     website: https://www.mohebi-associates.org/

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/MANUAL.md

@@ -1,6 +1,6 @@
 # DriftlessMap User Manual
 
-This manual applies to **DriftlessMap 1.5.0**.
+This manual applies to **DriftlessMap 1.6.1**.
 
 DriftlessMap - Histological E-data Registration in Brain Space - is a desktop
 application for aligning rodent histology with a reference atlas, reconstructing
@@ -107,7 +107,7 @@ purposes. See [Saving, loading, and exporting](#18-saving-loading-and-exporting)
 
 ### 2.1 Requirements
 
-DriftlessMap 1.5.0 requires:
+DriftlessMap 1.6.1 requires:
 
 - A 64-bit operating system and 64-bit Python 3.10 or newer.
 - Python 3.10-3.14 for the core application.
@@ -126,7 +126,7 @@ page. The macOS DMG (`-macOS-arm64.dmg`) is built for Apple Silicon; on an Intel
 Mac, use the developer installation below.
 The desktop builds include Python and all runtime dependencies. Windows users
 extract the entire ZIP and run `DriftlessMap.exe`; macOS users open the DMG and
-drag `DriftlessMap.app` to Applications. The 1.5.0 release is unsigned, so the
+drag `DriftlessMap.app` to Applications. The 1.6.1 release is unsigned, so the
 first launch may require Windows SmartScreen confirmation or Control-clicking
 the macOS app and choosing **Open**.
 
@@ -174,7 +174,7 @@ python -m pip --version
 python -c "import driftlessmap; print(driftlessmap.__version__)"
 ```
 
-The final command should print `1.5.0`.
+The final command should print `1.6.1`.
 
 ### 2.5 Launching DriftlessMap
 
@@ -714,7 +714,68 @@ probe, virus, cell, contour, and drawing transfer.
 4. Show **Volume + Histology** or **Slice + Histology**.
 5. Avoid resizing or rotating the source image after placing landmarks.
 
-### 8.2 Place paired landmarks
+### 8.2 Suggest the section and landmarks automatically
+
+DriftlessMap can propose a starting point for registration with a volume
+atlas. Both steps are suggestions: always review the result before
+transferring anything.
+
+**Atlas > Suggest Atlas Section...** compares the loaded histology with the
+atlas and ranks candidate sections:
+
+1. Load the volume atlas and the histology section. A single, whole section
+   on a plain background works best; the tissue outline is found by
+   thresholding.
+2. Choose **Atlas > Suggest Atlas Section...**. The comparison runs in the
+   background and usually takes a few seconds.
+3. The dialog reports the most likely plane (coronal, sagittal or horizontal)
+   and how clearly it was preferred (**clear**, **uncertain** or
+   **ambiguous**), the orientation the section needs, and up to six candidate
+   sections. Each shows your section on the left and the atlas on the right,
+   with its depth and cutting-angle tilt.
+4. Pick the candidate that looks best. Brain outlines are left-right
+   symmetric, so the hemisphere cannot be detected: choose **Other
+   hemisphere** if the section comes from the other side.
+5. Leave **Apply the suggested cutting-angle tilt** on to use the tilt, and
+   **Rotate/flip the histology to match** on to orient the image. Rotating
+   the histology resets its landmarks.
+6. Press **Apply**. DriftlessMap switches to the plane, shows the section and
+   sets the tilt. For coronal and horizontal sections the sagittal pivot is
+   moved to the midline.
+
+The plane is found from the outline, the depth mainly from internal anatomy,
+and the tilt from a small search of about ±6°. Damaged or partial sections,
+sections with more than one piece of tissue, and strongly uneven staining make
+suggestions less reliable.
+
+**Atlas > Propose Landmarks** then fits the displayed atlas slice to the
+section and fills the Triangulation tool with paired landmarks:
+
+1. Show the matching atlas slice and orient the histology to it, for example
+   with **Suggest Atlas Section...**. Remove any transform overlay first.
+2. Choose **Atlas > Propose Landmarks**. If landmarks already exist, you are
+   asked before they are replaced.
+3. DriftlessMap fits the outlines, then refines the fit on the image
+   intensities where that improves the match. It suggests up to 10 landmarks:
+   up to 5 at the sharpest tips and notches of the outline, snapped onto the
+   section outline, and the rest on strong internal edges that both images
+   show, such as the corpus callosum. It moves the boundary anchors with the
+   same fit. The landmarks are suggestions to confirm and edit.
+4. The status bar reports how many pairs are on the outline and how many are
+   on internal edges, and the outline overlap. The
+   Triangulation tool opens so you can check the mesh. Drag any landmark that
+   is off, add more where the anatomy needs them, and check mesh quality
+   (Section 8.5) before transferring.
+
+The fit follows the outline and the overall shape well, but internal
+boundaries can still be several voxels off. Treat the proposal as a first
+draft of the manual landmarks, not as a finished registration.
+
+The tutorial [Automatic Section Matching and Landmark Proposal](Tutorial/Registration_Related/automatic_section_and_landmarks.md)
+walks through both steps on a real section, with screenshots, and explains
+how each stage works.
+
+### 8.3 Place paired landmarks
 
 1. Activate Triangulation.
 2. Choose a point color visible in both windows.
@@ -741,7 +802,7 @@ Landmarks can be dragged. With Eraser active, clicking a numbered landmark
 deletes the corresponding point in both windows and renumbers the remaining
 pairs.
 
-### 8.3 Match boundary rectangles
+### 8.4 Match boundary rectangles
 
 The automatically generated outer points define the warp domain. After
 interior points are placed, use **Match Boundaries** when the atlas and
@@ -751,7 +812,7 @@ anchors while retaining the paired interior anatomy.
 For a volume atlas, boundary matching can derive the atlas extent from the
 nonzero label area. A slice atlas requires interior landmarks in both images.
 
-### 8.4 Evaluate mesh quality
+### 8.5 Evaluate mesh quality
 
 The Triangulation controls report:
 
@@ -773,7 +834,7 @@ To repair a mesh:
 - Confirm that pair order has not been confused.
 - Recheck the atlas slice and tilt.
 
-### 8.5 Create and refine an overlay
+### 8.6 Create and refine an overlay
 
 To overlay histology onto the atlas:
 
@@ -793,7 +854,7 @@ repeatedly warping an already transformed preview, preventing accumulated blur.
 Atlas labels and masks use nearest-neighbor mapping where discrete values must
 be preserved; histology display uses smooth interpolation.
 
-### 8.6 Transfer annotations
+### 8.7 Transfer annotations
 
 Once the registration is accepted:
 
@@ -812,7 +873,7 @@ Points outside the registration mesh cannot be assigned a valid atlas
 coordinate. DriftlessMap preserves or rejects them according to the data type and
 reports the count; do not silently treat them as registered.
 
-### 8.7 Save registration landmarks
+### 8.8 Save registration landmarks
 
 Use:
 
@@ -1488,6 +1549,8 @@ still read when a DriftlessMap setting has not been created.
 | Download Waxholm Rat Atlas | Download/process standard rat atlas. |
 | Download Allen Mice Atlas | Download/process Allen 10, 25, or 50 um atlas. |
 | Atlas Processor | Process a custom volume atlas. |
+| Suggest Atlas Section... | Rank atlas plane, section, tilt and orientation for the loaded histology. |
+| Propose Landmarks | Fit the shown atlas slice to the histology and fill in registration landmarks. |
 | Save/Load Triangulation Points | Write/read `.dmaptri`. |
 | Load Slice | Load a raw or processed 2D atlas plate. |
 | Register Slice Info | Set plane, dimensions, and Bregma distance. |

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: driftlessmap
-Version: 1.5.0
+Version: 1.6.1
 Summary: Interactive histology registration and brain-atlas mapping
 Author: Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, Mohebi & Associates, Ali Mohebi
 Author-email: Jingyi Guo Fuglstad <jingyi.g.fuglstad@gmail.com>
@@ -44,6 +44,7 @@ Requires-Dist: tifffile>=2024.7
 Requires-Dist: pandas<4,>=2.2
 Requires-Dist: natsort<9,>=8.4
 Requires-Dist: imagecodecs>=2024.6
+Requires-Dist: SimpleITK<3,>=2.3
 Provides-Extra: czi
 Requires-Dist: aicspylibczi>=3.3.1; python_version < "3.14" and extra == "czi"
 Provides-Extra: test
@@ -95,6 +96,7 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 
 - 2D and 3D visualization of volumetric brain atlases and arbitrary slices.
 - Interactive histology-to-atlas registration with local elastic deformation.
+- Automatic suggestions for the matching atlas section and starting landmarks.
 - Probe planning, reconstruction, contact mapping, and CSV export.
 - Drawing, cell, virus-expression, and user-defined object workflows.
 - Safe, versioned project and object archives.
@@ -102,7 +104,7 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 
 ## Installation
 
-DriftlessMap 1.5.0 is available as a desktop application for end users and as
+DriftlessMap 1.6.1 is available as a desktop application for end users and as
 a Python package for developers.
 
 ### Mode 1: desktop application for end users
@@ -110,10 +112,10 @@ a Python package for developers.
 No Python or Conda installation is required. Download the asset for your
 computer from [GitHub Releases](https://github.com/mohebi-n-associates/DriftlessMap/releases):
 
-- **Windows 64-bit:** download `DriftlessMap-1.5.0-Windows-x64.zip`, extract
+- **Windows 64-bit:** download `DriftlessMap-1.6.1-Windows-x64.zip`, extract
   the complete folder, and double-click `DriftlessMap.exe`. Do not move the
   executable out of its extracted folder.
-- **macOS (Apple Silicon):** download `DriftlessMap-1.5.0-macOS-arm64.dmg`,
+- **macOS (Apple Silicon):** download `DriftlessMap-1.6.1-macOS-arm64.dmg`,
   open it, and drag `DriftlessMap.app` to Applications. The application bundle
   includes the DriftlessMap icon and all Python dependencies. Intel Macs are
   not covered by the desktop build; use the Conda/pip installation below.
@@ -137,7 +139,7 @@ malware:
    required only for the first launch.
 
 Only use **Open Anyway** for a copy downloaded from the
-[official DriftlessMap 1.5.0 release](https://github.com/mohebi-n-associates/DriftlessMap/releases/tag/v1.5.0).
+[official DriftlessMap 1.6.1 release](https://github.com/mohebi-n-associates/DriftlessMap/releases/tag/v1.6.1).
 The official macOS DMG has this SHA-256 digest:
 
 ```text

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/README.md

@@ -38,6 +38,7 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 
 - 2D and 3D visualization of volumetric brain atlases and arbitrary slices.
 - Interactive histology-to-atlas registration with local elastic deformation.
+- Automatic suggestions for the matching atlas section and starting landmarks.
 - Probe planning, reconstruction, contact mapping, and CSV export.
 - Drawing, cell, virus-expression, and user-defined object workflows.
 - Safe, versioned project and object archives.
@@ -45,7 +46,7 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 
 ## Installation
 
-DriftlessMap 1.5.0 is available as a desktop application for end users and as
+DriftlessMap 1.6.1 is available as a desktop application for end users and as
 a Python package for developers.
 
 ### Mode 1: desktop application for end users
@@ -53,10 +54,10 @@ a Python package for developers.
 No Python or Conda installation is required. Download the asset for your
 computer from [GitHub Releases](https://github.com/mohebi-n-associates/DriftlessMap/releases):
 
-- **Windows 64-bit:** download `DriftlessMap-1.5.0-Windows-x64.zip`, extract
+- **Windows 64-bit:** download `DriftlessMap-1.6.1-Windows-x64.zip`, extract
   the complete folder, and double-click `DriftlessMap.exe`. Do not move the
   executable out of its extracted folder.
-- **macOS (Apple Silicon):** download `DriftlessMap-1.5.0-macOS-arm64.dmg`,
+- **macOS (Apple Silicon):** download `DriftlessMap-1.6.1-macOS-arm64.dmg`,
   open it, and drag `DriftlessMap.app` to Applications. The application bundle
   includes the DriftlessMap icon and all Python dependencies. Intel Macs are
   not covered by the desktop build; use the Conda/pip installation below.
@@ -80,7 +81,7 @@ malware:
    required only for the first launch.
 
 Only use **Open Anyway** for a copy downloaded from the
-[official DriftlessMap 1.5.0 release](https://github.com/mohebi-n-associates/DriftlessMap/releases/tag/v1.5.0).
+[official DriftlessMap 1.6.1 release](https://github.com/mohebi-n-associates/DriftlessMap/releases/tag/v1.6.1).
 The official macOS DMG has this SHA-256 digest:
 
 ```text

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/UpdateLog.md

@@ -1,5 +1,15 @@
 # Update Log
 
+### 28th September 2026
+##### DriftlessMap 1.6.1
+
+Fixes **Show Boundary**, which drew atlas region boundaries almost black and therefore invisibly. **Propose Landmarks** now suggests up to 10 landmarks on features both images show (outline tips and notches, shared internal edges) instead of about 36. Adds a tutorial for the automatic section and landmark suggestions.
+
+### 27th September 2026
+##### DriftlessMap 1.6.0
+
+Adds **Atlas > Suggest Atlas Section...**, which suggests the atlas plane, section, tilt and histology orientation for a loaded section. Also adds **Atlas > Propose Landmarks**, which fits the shown atlas slice to the histology and fills in registration landmarks for review. SimpleITK is now a required dependency.
+
 ### 27th September 2026
 ##### DriftlessMap 1.5.0
 

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/WhatsNew.md

@@ -3,6 +3,80 @@
 This cumulative release history is maintained as a single document. New
 releases are added at the top; earlier release notes remain below them.
 
+## DriftlessMap 1.6.1
+
+Release date: 28 September 2026
+
+### Fixed
+
+- **Show Boundary** now draws atlas region boundaries in white. Since the
+  boundary images were stored as one byte per pixel, they had been drawn
+  almost black, so the button appeared to do nothing.
+
+### Changed
+
+- **Propose Landmarks** now suggests up to 10 landmarks instead of about 36,
+  each on a feature you can see and check in both images:
+  - up to 5 at the sharpest tips and notches of the brain outline, snapped
+    onto the section outline;
+  - the rest on strong internal edges that both images show, such as the
+    corpus callosum and the ventricles.
+
+  An edge seen in only one image is never chosen: an atlas region border in
+  uniform-looking tissue, or a dye track in the section. The status bar says
+  how many points are on the outline and how many are internal. Confirm or
+  drag each point, and add more by hand where the anatomy needs them.
+
+### Documentation
+
+- A new tutorial, [Automatic Section Matching and Landmark Proposal](Tutorial/Registration_Related/automatic_section_and_landmarks.md),
+  walks through **Suggest Atlas Section...** and **Propose Landmarks** on a
+  real sagittal section and explains how each stage works.
+
+## DriftlessMap 1.6.0
+
+Release date: 27 September 2026
+
+This release adds two assistants for volume-atlas registration. They suggest
+where a section sits in the atlas and propose starting landmarks. You review
+and confirm every suggestion; nothing is transferred automatically. Files
+saved by 1.5.0 open unchanged, and nothing needs to be re-exported.
+
+### Suggest Atlas Section
+
+**Atlas > Suggest Atlas Section...** compares the loaded histology with the
+volume atlas and suggests the section it came from:
+
+- the plane (coronal, sagittal or horizontal), found from the tissue outline,
+  with a note on how clearly it was preferred;
+- the orientation the histology needs (rotation and flip);
+- the depth, ranked mainly by internal anatomy;
+- a small cutting-angle tilt, searched within about ±6°.
+
+A dialog shows up to six candidates as side-by-side thumbnails. Choose one and
+press **Apply**: DriftlessMap switches the plane, shows the section and sets
+the tilt, and can also rotate or flip the histology to match. Because brain
+outlines are left-right symmetric, you choose the hemisphere yourself.
+
+### Propose Landmarks
+
+**Atlas > Propose Landmarks** fits the displayed atlas slice to the section.
+It first fits the outlines, then refines the fit on image intensities where
+that improves the match. It then fills the Triangulation tool with about 36
+paired landmarks and moves the boundary anchors with the same fit. Drag,
+add or delete landmarks as usual before transferring. Existing landmarks are
+replaced only after you confirm.
+
+The fit follows the outline and overall shape well. Internal boundaries can
+still be several voxels off, so treat the proposal as a first draft.
+
+### Other changes
+
+- DriftlessMap now requires SimpleITK, which the desktop builds and a normal
+  `pip install` include.
+- The Registering chapter of the manual gains Section 8.2, which describes
+  both assistants. Later sections in that chapter are renumbered.
+
 ## DriftlessMap 1.5.0
 
 Release date: 27 September 2026

{driftlessmap-1.5.0 → driftlessmap-1.6.1}/driftlessmap/app.py

@@ -141,7 +141,10 @@ from .probe_reconstruction import (
     source_vox_to_herbs_vox,
 )
 from .roi_analysis import build_drawing_roi_info
+from .atlas_matching import suggest_sections
+from .auto_registration import propose_landmarks
 from .background import run_in_background
+from .section_suggestion_dialog import SectionSuggestionDialog
 from .landmarks import LANDMARK_FIELDS, LandmarkModel, triangulation_payload_error
 from .project_io import (
     default_working_atlas_data,
@@ -525,6 +528,8 @@ class DriftlessMap(QMainWindow, FORM_Main):
         self.actionRegister_Slice_Info.triggered.connect(self.register_slice_info)
         self.actionSave_Slice.triggered.connect(self.save_processed_slice)
         self.actionSwitch_Atlas.triggered.connect(self.switch_atlas)
+        self.actionSuggest_Atlas_Section.triggered.connect(self.suggest_atlas_section)
+        self.actionPropose_Landmarks.triggered.connect(self.propose_registration_landmarks)
         self.actionBregma_Picker.setCheckable(True)
         self.actionBregma_Picker.triggered.connect(self.pick_bregma)
         self.actionCreate_Slice_Layer.triggered.connect(self.process_slice)
@@ -1756,6 +1761,200 @@ class DriftlessMap(QMainWindow, FORM_Main):
                 "Current Slice is saved successfully.", self.normal_color
             )
 
+    def suggest_atlas_section(self):
+        """Suggest and apply the atlas plane, slice and tilt for the section."""
+        if (
+            self.current_atlas != "volume"
+            or self.atlas_view.atlas_data is None
+            or self.atlas_view.atlas_label is None
+        ):
+            self.print_message(
+                "Load a volume atlas before suggesting an atlas section.",
+                self.error_message_color,
+            )
+            return
+        if self.image_view.current_img is None:
+            self.print_message(
+                "Load a histology section before suggesting an atlas section.",
+                self.error_message_color,
+            )
+            return
+        view = self.atlas_view
+        section = np.asarray(self.image_view.current_img)
+        midline = int(view.origin_3d[0])
+        # Tilts for coronal/horizontal pivot on the midline (see above); the
+        # sagittal pivot is its own page, so its value here does not matter.
+        pivot = (int(view.current_coronal_index), midline,
+                 int(view.current_horizontal_index))
+        try:
+            report = run_in_background(
+                self,
+                "Comparing the section with the atlas...",
+                suggest_sections,
+                section,
+                view.atlas_label,
+                view.atlas_data,
+                midline,
+                pivot,
+            )
+        except ValueError as exc:
+            self.print_message(
+                "No atlas section could be suggested: {}".format(exc),
+                self.error_message_color,
+            )
+            return
+        if not report.suggestions:
+            self.print_message(
+                "No atlas section could be suggested for this image.",
+                self.error_message_color,
+            )
+            return
+        dialog = SectionSuggestionDialog(
+            report, section, view.atlas_data, pivot, view.vox_size_um, self
+        )
+        if dialog.exec() != QDialog.DialogCode.Accepted:
+            return
+        choice = dialog.choice()
+        if choice is not None:
+            self.apply_section_suggestion(*choice)
+
+    def apply_section_suggestion(self, plane, index, orientation, tilt, rotate_histology):
+        """Show ``plane``/``index`` at ``tilt`` and orient the histology."""
+        view = self.atlas_view
+        if rotate_histology:
+            for _ in range(orientation.quarter_turns % 4):
+                self.image_view.image_90_counter_rotate()
+            if orientation.mirrored:
+                self.image_view.image_horizon_flip()
+        buttons = {"coronal": view.section_rabnt1, "sagittal": view.section_rabnt2,
+                   "horizontal": view.section_rabnt3}
+        pages = {"coronal": view.cpage_ctrl, "sagittal": view.spage_ctrl,
+                 "horizontal": view.hpage_ctrl}
+        rotations = {"coronal": view.crotation_ctrl, "sagittal": view.srotation_ctrl,
+                     "horizontal": view.hrotation_ctrl}
+        buttons[plane].setChecked(True)
+        if plane in ("coronal", "horizontal"):
+            view.spage_ctrl.set_val(int(view.origin_3d[0]))
+        pages[plane].set_val(int(index))
+        rotation = rotations[plane]
+        rotation.h_spinbox.setValue(float(tilt[0]))
+        rotation.v_spinbox.setValue(float(tilt[1]))
+        self.print_message(
+            "Showing the suggested {} slice {} at tilt ({:+.1f}°, {:+.1f}°). "
+            "Check the match before placing landmarks.".format(
+                plane, index, tilt[0], tilt[1]
+            ),
+            self.normal_color,
+        )
+
+    def propose_registration_landmarks(self):
+        """Register the section to the displayed atlas slice and propose
+        paired landmarks, which the user reviews with the triangulation tool."""
+        if (
+            self.current_atlas != "volume"
+            or self.atlas_view.atlas_data is None
+            or self.atlas_view.working_atlas.label_data is None
+        ):
+            self.print_message(
+                "Show a volume atlas slice before proposing landmarks.",
+                self.error_message_color,
+            )
+            return
+        if self.image_view.current_img is None:
+            self.print_message(
+                "Load a histology section before proposing landmarks.",
+                self.error_message_color,
+            )
+            return
+        if self.a2h_transferred or self.h2a_transferred:
+            self.print_message(
+                "Remove the current transform overlay before proposing landmarks.",
+                self.error_message_color,
+            )
+            return
+        if self.atlas_tri_inside_data or self.histo_tri_inside_data:
+            reply = QMessageBox.question(
+                self,
+                "Propose Landmarks",
+                "Replace the current registration landmarks with proposed ones?",
+                QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
+                QMessageBox.StandardButton.No,
+            )
+            if reply != QMessageBox.StandardButton.Yes:
+                return
+        stack = self.atlas_view.working_atlas
+        try:
+            proposal = run_in_background(
+                self,
+                "Registering the section to the atlas slice...",
+                propose_landmarks,
+                np.asarray(stack.img.image),
+                np.asarray(stack.label_data),
+                np.asarray(self.image_view.current_img),
+                boundary_points=np.asarray(self.atlas_tri_onside_data, dtype=float),
+            )
+        except (ValueError, RuntimeError) as exc:
+            self.print_message(
+                "Landmarks could not be proposed: {}".format(exc),
+                self.error_message_color,
+            )
+            return
+        if len(proposal.atlas_points) < 3:
+            self.print_message(
+                "Too few landmarks could be proposed; place them by hand.",
+                self.error_message_color,
+            )
+            return
+        self.apply_landmark_proposal(proposal)
+
+    def apply_landmark_proposal(self, proposal):
+        """Replace interior landmarks with a proposal and show them."""
+        self._invalidate_triangulation(clear_topology=True)
+        self.atlas_tri_inside_data = [
+            [round(float(x), 2), round(float(y), 2)] for x, y in proposal.atlas_points
+        ]
+        self.histo_tri_inside_data = [
+            [round(float(x), 2), round(float(y), 2)] for x, y in proposal.histology_points
+        ]
+        if len(proposal.boundary_points) == len(self.atlas_tri_onside_data):
+            # Carry the mesh frame through the fit too, so the fixed frame
+            # points do not contradict the interior landmarks.
+            self.histo_tri_onside_data = [
+                [round(float(x), 2), round(float(y), 2)]
+                for x, y in proposal.boundary_points
+            ]
+        self.atlas_tri_data = self.atlas_tri_onside_data + self.atlas_tri_inside_data
+        self.histo_tri_data = self.histo_tri_onside_data + self.histo_tri_inside_data
+        self.atlas_view.working_atlas.image_dict["tri_pnts"].setData(
+            pos=np.asarray(self.atlas_tri_data)
+        )
+        self.image_view.img_stacks.image_dict["tri_pnts"].setData(
+            pos=np.asarray(self.histo_tri_data)
+        )
+        self._refresh_triangulation_text("atlas")
+        self._refresh_triangulation_text("image")
+        # Show the proposal in the triangulation tool, ready for editing.
+        button = self.tool_box.checkable_btn_dict["triang_btn"]
+        if not button.isChecked():
+            button.setChecked(True)
+            self.triang_btn_clicked()
+        if self.tool_box.triang_vis_btn.isChecked():
+            self.update_atlas_tri_lines()
+            self.update_histo_tri_lines()
+        else:
+            self._build_triangulation_registration(strict=False, show_error=False)
+        stage = "outline and intensity" if proposal.deformable_used else "outline"
+        on_outline = sum(kind == "outline" for kind in proposal.kinds)
+        self.print_message(
+            "Suggested {} landmark pairs ({} on the outline, {} on internal edges) "
+            "from the {} fit (outline overlap {:.2f}). Confirm or drag each one "
+            "before transferring.".format(
+                len(proposal.atlas_points), on_outline,
+                len(proposal.atlas_points) - on_outline, stage, proposal.overlap_final
+            ),
+            self.normal_color,
+        )
+
     def switch_atlas(self):
         if (
             self.atlas_view.atlas_data is None
@@ -2929,7 +3128,7 @@ class DriftlessMap(QMainWindow, FORM_Main):
                         True
                     )
                 if (
-                    self.atlas_tri_inside_data
+                    self.working_atlas_text
                     and not self.working_atlas_text[0].isVisible()
                 ):
                     for i in range(len(self.working_atlas_text)):
@@ -2938,7 +3137,7 @@ class DriftlessMap(QMainWindow, FORM_Main):
                 if not self.image_view.img_stacks.image_dict["tri_pnts"].isVisible():
                     self.image_view.img_stacks.image_dict["tri_pnts"].setVisible(True)
                 if (
-                    self.histo_tri_inside_data
+                    self.working_img_text
                     and not self.working_img_text[0].isVisible()
                 ):
                     for i in range(len(self.working_img_text)):
@@ -2950,7 +3149,7 @@ class DriftlessMap(QMainWindow, FORM_Main):
                         False
                     )
                 if (
-                    self.atlas_tri_inside_data
+                    self.working_atlas_text
                     and self.working_atlas_text[0].isVisible()
                 ):
                     for i in range(len(self.working_atlas_text)):
@@ -2958,7 +3157,7 @@ class DriftlessMap(QMainWindow, FORM_Main):
             if self.histo_tri_data:
                 if self.image_view.img_stacks.image_dict["tri_pnts"].isVisible():
                     self.image_view.img_stacks.image_dict["tri_pnts"].setVisible(False)
-                if self.histo_tri_inside_data and self.working_img_text[0].isVisible():
+                if self.working_img_text and self.working_img_text[0].isVisible():
                     for i in range(len(self.working_img_text)):
                         self.working_img_text[i].setVisible(False)