Seg for lost IDs 2 by Teranis · Pull Request #1098 · SchmollerLab/Cell_ACDC

Teranis · 2026-05-09T19:45:57Z

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Copilot

Pull request overview

This PR extends “Segmentation for lost IDs” to support selecting/running multiple segmentation models via a persisted “recipe”, adds a per-GUI cache for imported segmentation modules, and improves logging robustness for Unicode output.

Changes:

Add multi-model selection UI (including “select last selection/recipe”) and persist/load a JSON recipe for “Seg for lost IDs”.
Update the SegForLostIDs worker to iterate through multiple model configurations and pass explicit model/post-processing settings into single_cell_seg.
Harden stdout/file logging against Unicode encoding issues and set UTF-8 encoding for log files.

Reviewed changes

Copilot reviewed 5 out of 17 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
cellacdc/workers.py	Refactors SegForLostIDs worker to run multiple models and reuse imported modules; updates regionprops usage.
cellacdc/segm_utils.py	Updates `single_cell_seg` signature to accept explicit model and post-processing kwargs (instead of a GUI “win”).
cellacdc/myutils.py	Makes logger output more resilient to Unicode and writes log files as UTF-8.
cellacdc/gui.py	Adds multi-model selection + recipe persistence/loading + module cache initialization for SegForLostIDs.
cellacdc/apps.py	Adds new multi-pick model selection widgets and extends `QDialogSelectModel` for multi-selection workflows.

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…Cell_ACDC into seg_for_lost_IDs_2

Copilot

Pull request overview

Copilot reviewed 5 out of 17 changed files in this pull request and generated 2 comments.

Copilot

Pull request overview

Copilot reviewed 5 out of 17 changed files in this pull request and generated 4 comments.

Copilot

Pull request overview

Copilot reviewed 6 out of 18 changed files in this pull request and generated 5 comments.

ElpadoCan

Things found upon review:

Circular import of load.loadData in core.py
Move apps.MultiPickListWidget to widgets.MultiPickListWidget
Use the same stylesheet found in cellacdc._palettes.ListWidgetStyleSheet for the new MultiPickListWidget

Copilot

Pull request overview

Copilot reviewed 11 out of 23 changed files in this pull request and generated 5 comments.

+                    original_bbox_lab_cleared_borders = skimage.segmentation.clear_border(original_bbox_lab)
+                    box_model_lab = model_lab[box_x_min:box_x_max, box_y_min:box_y_max]

                # original_bbox_lab[np.isin(original_bbox_lab, IDs)] = 0 should be a given. If not seg for lost IDs this recommended


+            if (
+                len(selected_models) == 1
+                and selected_models[0] == 'Automatic thresholding'
+            ):
+                self.selectedModel = 'thresholding'
+            else:
+                self.selectedModel = selected_models


Copilot

Pull request overview

Copilot reviewed 12 out of 24 changed files in this pull request and generated 6 comments.

+    monkeypatch.setattr(worker, 'emitSigAskInit', lambda: None)
+    monkeypatch.setattr(worker, 'emitSigAskInstallGPU', lambda base_model_name, use_gpu: None)
+    monkeypatch.setattr(worker, 'emitSigUpdateRP', lambda wl_update=True, wl_track_og_curr=False: None)
+    monkeypatch.setattr(worker, 'emitSigStoreData', lambda autosave=True: None)
+    monkeypatch.setattr(worker, 'emitTrackManuallyAddedObject', lambda *args, **kwargs: None)
+    monkeypatch.setattr(myutils, 'import_segment_module', lambda base_model_name: SimpleNamespace(Model=ThresholdingModel))
+    monkeypatch.setattr(myutils, 'init_segm_model', lambda acdcSegment, posData, init_kwargs_new: ThresholdingModel())
+
+    worker.run()


+                if 'device' in init_kwargs:
+                    init_kwargs_new = dict(init_kwargs_new, device='cpu')
+                if 'use_gpu' in init_kwargs:
+                    init_kwargs_new = dict(init_kwargs_new, use_gpu=False)


+                            target_ID = segm_utils.get_best_overlapping_label(
+                                prev_bbox_lab,
+                                obj,
+                                missing_IDs_global,
+                            )
+                            if target_ID is None:
+                                continue
+
+                            filtered_IDs.append(obj.label)
+                            relabeled_IDs[obj.label] = target_ID


+                self._stdout.write(text.encode(
+                    self._stdout.encoding, errors='replace'
+                ).decode(self._stdout.encoding))


+    def _addCounterWidget(self, label, item):
+        rowWidget = QWidget()
+        rowLayout = QHBoxLayout(rowWidget)
+        rowLayout.setContentsMargins(4, 0, 4, 0)
+        rowLayout.setSpacing(6)
+
+        nameLabelPlaceholder = QSpacerItem(2, 0)
+        minusBtn = QPushButton('-')
+        plusBtn = QPushButton('+')
+        countLabel = QLabel(str(self._countMap.get(label, 0)))
+
+        minusBtn.setFixedWidth(24)
+        plusBtn.setFixedWidth(24)
+        countLabel.setMinimumWidth(20)
+        countLabel.setAlignment(Qt.AlignCenter)
+
+        minusBtn.clicked.connect(lambda _, lbl=label: self.removeSelection(lbl))
+        plusBtn.clicked.connect(lambda _, lbl=label: self.addSelection(lbl))
+
+        rowLayout.addItem(nameLabelPlaceholder)
+        rowLayout.addStretch(1)
+        rowLayout.addWidget(minusBtn)
+        rowLayout.addWidget(countLabel)
+        rowLayout.addWidget(plusBtn)


+            'Use this dialog to define the segmentation workflow used for '
+            'resegmenting local neighborhood lost IDs. Other already segmented cells are filled '
+            'with background, which makes even dimm cells seem bright after '
+            'rescaling before resegmentation. This is especially usefull for '
+            'cells which have varying intensities over time, like FUCCI cells. <br><br>'


Copilot

Pull request overview

Copilot reviewed 12 out of 24 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

cellacdc/segm_utils.py:326

single_cell_seg currently assigns a fresh new_unique_ID to every segmented object in the bbox. This prevents the SegForLostIDs flow from recovering the original (missing) IDs, even though get_best_overlapping_label was added for this purpose.

Instead, for each segmented object, map it back to the best-overlapping label in the previous-frame bbox among the requested IDs; only fall back to new_unique_ID when no allowed overlap exists.

        rp_model_lab = regionprops.acdcRegionprops(box_model_lab,precache_centroids=False)
        for obj in rp_model_lab:
            box_curr_lab_other_IDs[box_model_lab == obj.label] = new_unique_ID
            assigned_IDs.append(new_unique_ID)
            new_unique_ID += 1

    def emitSigUpdateRP(self, wl_track_og_curr, wl_update):
        self.mutex.lock()
        self.sigUpdateRP.emit(wl_track_og_curr, wl_update)
        self.waitCond.wait(self.mutex)
        self.mutex.unlock()


+    monkeypatch.setattr(myutils, 'import_segment_module', lambda base_model_name: SimpleNamespace(Model=ThresholdingModel))
+    monkeypatch.setattr(myutils, 'init_segm_model', lambda acdcSegment, posData, init_kwargs_new: ThresholdingModel())
+
+    worker.run()


Teranis added 2 commits May 7, 2026 18:45

WIP: seg for lost IDs with different models

7fffaf7

Merge branch 'optimizations' into seg_for_lost_IDs_2

7ac4807

Teranis changed the title ~~Seg for lost i ds 2~~ Seg for lost IDs 2 May 9, 2026

Teranis requested a review from Copilot May 9, 2026 19:46

Copilot started reviewing on behalf of Teranis May 9, 2026 19:46 View session

ci: update precompiled Cython extensions [skip ci]

0a9522c

Copilot AI reviewed May 9, 2026

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Comment thread cellacdc/apps.py Outdated

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/segm_utils.py Outdated

Teranis added 2 commits May 9, 2026 22:06

fix: copilot comments

3cb1226

Merge branch 'seg_for_lost_IDs_2' of https://github.com/SchmollerLab/…

a7d63af

…Cell_ACDC into seg_for_lost_IDs_2

Teranis requested a review from Copilot May 9, 2026 20:07

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Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/apps.py

feat: add cumstom model bettere handled

39ab0b3

Teranis requested a review from Copilot May 9, 2026 20:51

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Comment thread cellacdc/apps.py

Comment thread cellacdc/apps.py Outdated

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/segm_utils.py

fix: copilot comments

767f0da

Teranis requested a review from Copilot May 9, 2026 21:07

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Comment thread cellacdc/workers.py

Comment thread cellacdc/workers.py Outdated

Comment thread cellacdc/segm_utils.py

Comment thread cellacdc/gui.py

Comment thread cellacdc/apps.py

ElpadoCan reviewed May 11, 2026

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fix: copilot comments, UI appearance, bugs

4c1dbb3

Teranis requested a review from Copilot May 11, 2026 13:35

Copilot started reviewing on behalf of Teranis May 11, 2026 13:35 View session

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Teranis added 4 commits May 11, 2026 19:22

fix: automatic thresholding

8ff1cf6

fix: github comments, thresholding

4c1de3d

feat: use any fluo channel for segmentation

a34b775

feat: info label for select model

a58d90e

Teranis requested a review from Copilot May 12, 2026 09:31

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Teranis added 2 commits May 12, 2026 15:53

fix: dragging scrollbar

616f2ad

feat: better debug mode, refactoring old convoluted code

c79938b

Teranis requested a review from Copilot June 16, 2026 14:14

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