.gitignore
AGENTS.md
CHANGES.md
CLAUDE.md
CONTRIBUTING.md
GETTING_STARTED.md
INSTALLATION.md
LICENSE
MANIFEST.in
README.md
RELEASE.md
SCRIPTING.md
pyproject.toml
setup.py
.claude/agents/autolamella-auditor.md
.claude/agents/autolamella-investigator.md
.claude/agents/autolamella-verifier.md
.claude/fibsem-agent/playbooks/autolamella-correlative.yaml
.claude/fibsem-agent/playbooks/autolamella.yaml
.claude/fibsem-agent/playbooks/fibsem-agent.yaml
.claude/fibsem-agent/playbooks/fibsem-experiment.yaml
.claude/skills/autolamella/SKILL.md
.claude/skills/autolamella/read_record.py
.claude/skills/autolamella-assistant/SKILL.md
.claude/skills/autolamella-coincidence-milling/SKILL.md
.claude/skills/autolamella-correlative/SKILL.md
.claude/skills/autolamella-lead/SKILL.md
.claude/skills/autolamella-polishing/SKILL.md
.claude/skills/fibsem-agent/SKILL.md
.claude/skills/fibsem-experiment/SKILL.md
.claude/skills/getting-started-dev/SKILL.md
.claude/skills/linear/SKILL.md
.claude/skills/new-widget/SKILL.md
.claude/skills/review-changes/SKILL.md
.claude/skills/review-widget/SKILL.md
.claude/skills/screen-grids/SKILL.md
.github/scripts/check_pr_body.py
.github/workflows/pr-body.yml
.github/workflows/publish.yml
.github/workflows/python-package.yml
constraints/odemis.txt
demos/README.md
demos/autolamella/demo_coincidence_viewer.py
demos/autolamella/demo_confirm_run_workflow_dialog.py
demos/autolamella/demo_lamella_card.py
demos/autolamella/demo_lamella_list.py
demos/autolamella/demo_lamella_name_list_widget.py
demos/autolamella/demo_lamella_task_image_widget.py
demos/autolamella/demo_lamella_workflow.py
demos/autolamella/demo_selected_lamella.py
demos/autolamella/demo_workflow_config.py
demos/autolamella/demo_workflow_task_editor_widget.py
demos/autolamella/demo_workflow_timeline_animation.py
demos/canvas/demo_active_overlay_mode.py
demos/canvas/demo_alignment_overlay.py
demos/canvas/demo_canvas_modifiers.py
demos/canvas/demo_detection_overlay.py
demos/canvas/demo_quad_view.py
demos/canvas/demo_real_space_canvas.py
demos/correlation/demo_correlation_canvas.py
demos/correlation/demo_correlation_fm_canvas.py
demos/correlation/demo_correlation_setup_section.py
demos/correlation/demo_correlation_tab_widget.py
demos/correlation/demo_correlation_v2.py
demos/fm/demo_autofocus_widget.py
demos/fm/demo_channel_list_widget.py
demos/fm/demo_fm_canvas.py
demos/fm/demo_fm_overview_widget.py
demos/fm/demo_fm_sparse_selection_dialog.py
demos/fm/demo_line_plot.py
demos/fm/demo_plot_autofocus.py
demos/imaging/demo_alignment_comparison.py
demos/imaging/demo_alignment_plot_v2.py
demos/imaging/demo_drawing_widget.py
demos/imaging/demo_tile_order_strategies.py
demos/milling/demo_milling_overlay.py
demos/milling/demo_milling_settings_widget.py
demos/milling/demo_milling_stage_list.py
demos/milling/demo_milling_stages_widget.py
demos/milling/demo_milling_task_config_widget.py
demos/milling/demo_milling_task_viewer_widget.py
demos/milling/demo_pattern_settings_widget.py
demos/widgets/demo_countdown_progress.py
demos/widgets/demo_dual_beam_widget.py
demos/widgets/demo_hooks_manual.py
demos/widgets/demo_icon_tool_button.py
demos/widgets/demo_image_settings_widget.py
demos/widgets/demo_overview_widget.py
demos/widgets/demo_progress_bar.py
demos/widgets/demo_progress_widget.py
demos/widgets/demo_reference_image_parameters_widget.py
demos/widgets/demo_saved_position_widget.py
demos/widgets/demo_spinner_icon.py
demos/widgets/demo_toast.py
demos/widgets/demo_vertical_tab_widget.py
docs/app-server.md
docs/gateway.md
docs/simulator.md
docs/brand/icons/.gitignore
docs/brand/icons/liftout.svg
docs/brand/icons/volume.svg
docs/developers/README.md
docs/developers/devices.md
docs/developers/extending.md
docs/developers/getting-started.md
docs/developers/render_simulator_examples.py
docs/developers/render_user_guide.py
docs/developers/screenshot-harness.md
docs/img/simulator/beams.png
docs/img/simulator/cell_types.png
docs/img/simulator/film.png
docs/img/simulator/fluorescence.png
docs/img/simulator/holder.png
docs/img/simulator/milling.png
docs/img/simulator/triplet.png
example/autolamella.py
example/example.ipynb
example/example.py
example/example_imaging.py
example/example_milling.py
example/example_movement.py
example/example_notebook.ipynb
example/lithography.py
example/profile.bmp
example/profile.npy
example/protocol_autolamella.yaml
example/protocol_lithography.yaml
example/protocol_slice_and_view.yaml
example/slice_and_view.py
examples/scripts/describe_lamellae.py
examples/scripts/export_summary.py
examples/scripts/survey_positions.py
external/application_files/autolamella.xml
external/application_files/cryo_Pt_dep.xml
fibsem/__init__.py
fibsem/_timing.py
fibsem/acquire.py
fibsem/acting.py
fibsem/cancellation.py
fibsem/cli.py
fibsem/config.py
fibsem/constants.py
fibsem/control.py
fibsem/conversions.py
fibsem/extras.py
fibsem/guided_setup.py
fibsem/hooks.py
fibsem/image_format.py
fibsem/keystore.py
fibsem/knowledge.py
fibsem/logo.py
fibsem/microscope.py
fibsem/paths.py
fibsem/progress.py
fibsem/saved_positions.py
fibsem/schema.py
fibsem/scripting.py
fibsem/session_state.py
fibsem/state_move.py
fibsem/timing.py
fibsem/transformations.py
fibsem/unreleased.py
fibsem/update_check.py
fibsem/utils.py
fibsem/vendor_libraries.py
fibsem/versioning.py
fibsem.egg-info/PKG-INFO
fibsem.egg-info/SOURCES.txt
fibsem.egg-info/dependency_links.txt
fibsem.egg-info/entry_points.txt
fibsem.egg-info/requires.txt
fibsem.egg-info/top_level.txt
fibsem/ai/__init__.py
fibsem/ai/agent/__init__.py
fibsem/ai/agent/blocklist.py
fibsem/ai/agent/calls.py
fibsem/ai/agent/code_mode.py
fibsem/ai/agent/drawing.py
fibsem/ai/agent/harness.py
fibsem/ai/agent/levels.py
fibsem/ai/agent/library.py
fibsem/ai/agent/manager.py
fibsem/ai/agent/mirror.py
fibsem/ai/agent/now.py
fibsem/ai/agent/pictures.py
fibsem/ai/agent/playbooks.py
fibsem/ai/agent/recent.py
fibsem/ai/agent/reminders.py
fibsem/ai/agent/session.py
fibsem/ai/agent/sources.py
fibsem/ai/agent/subagents.py
fibsem/ai/agent/suggestions.py
fibsem/ai/agent/usage.py
fibsem/ai/agent/watch.py
fibsem/ai/agent/catalog/__init__.py
fibsem/ai/agent/catalog/analysis.py
fibsem/ai/agent/catalog/app.py
fibsem/ai/agent/catalog/coating.py
fibsem/ai/agent/catalog/describe.py
fibsem/ai/agent/catalog/grids.py
fibsem/ai/agent/catalog/imaging.py
fibsem/ai/agent/catalog/items.py
fibsem/ai/agent/catalog/knowledge.py
fibsem/ai/agent/catalog/microscope.py
fibsem/ai/agent/catalog/milling.py
fibsem/ai/agent/catalog/spec.py
fibsem/ai/agent/mcp/README.md
fibsem/ai/agent/mcp/__init__.py
fibsem/ai/agent/mcp/sidecar.py
fibsem/alerts/__init__.py
fibsem/alerts/rules.py
fibsem/alerts/service.py
fibsem/alerts/slack.py
fibsem/alignment/__init__.py
fibsem/alignment/coincidence.py
fibsem/alignment/coincidence_target.py
fibsem/alignment/methods.py
fibsem/alignment/plotting.py
fibsem/applications/__init__.py
fibsem/applications/autolamella/__init__.py
fibsem/applications/autolamella/config.py
fibsem/applications/autolamella/config_edits.py
fibsem/applications/autolamella/experiment_setup.py
fibsem/applications/autolamella/hook_defaults.py
fibsem/applications/autolamella/launch.py
fibsem/applications/autolamella/overview_figure.py
fibsem/applications/autolamella/poses.py
fibsem/applications/autolamella/reference_images.py
fibsem/applications/autolamella/run_edits.py
fibsem/applications/autolamella/scripting.py
fibsem/applications/autolamella/structures.py
fibsem/applications/autolamella/task_outputs.py
fibsem/applications/autolamella/protocol/__init__.py
fibsem/applications/autolamella/protocol/constants.py
fibsem/applications/autolamella/protocol/task-protocol-waffle.yaml
fibsem/applications/autolamella/protocol/task-protocol.yaml
fibsem/applications/autolamella/protocol/development/task-protocol-coincidence.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-liftout.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-on-grid.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-serial-liftout.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-trench.yaml
fibsem/applications/autolamella/protocol/legacy/protocol-waffle.yaml
fibsem/applications/autolamella/server/__init__.py
fibsem/applications/autolamella/server/context.py
fibsem/applications/autolamella/server/replay.py
fibsem/applications/autolamella/tools/__init__.py
fibsem/applications/autolamella/tools/event_tables.py
fibsem/applications/autolamella/tools/grid_report.py
fibsem/applications/autolamella/tools/grid_report_html.py
fibsem/applications/autolamella/tools/ml_export.py
fibsem/applications/autolamella/tools/notebook.ipynb
fibsem/applications/autolamella/tools/pdf_export.py
fibsem/applications/autolamella/tools/replay.py
fibsem/applications/autolamella/tools/report_v2.py
fibsem/applications/autolamella/ui/__init__.py
fibsem/applications/autolamella/ui/header.py
fibsem/applications/autolamella/ui/launch.py
fibsem/applications/autolamella/ui/menu_bar.py
fibsem/applications/autolamella/ui/window.py
fibsem/applications/autolamella/ui/coincidence/__init__.py
fibsem/applications/autolamella/ui/coincidence/confirmation.py
fibsem/applications/autolamella/ui/coincidence/menu.py
fibsem/applications/autolamella/ui/coincidence/viewer.py
fibsem/applications/autolamella/ui/common/__init__.py
fibsem/applications/autolamella/ui/common/cards.py
fibsem/applications/autolamella/ui/common/lamella_display.py
fibsem/applications/autolamella/ui/dialogs/__init__.py
fibsem/applications/autolamella/ui/dialogs/create_experiment.py
fibsem/applications/autolamella/ui/dialogs/load_experiment.py
fibsem/applications/autolamella/ui/dialogs/overview_plot.py
fibsem/applications/autolamella/ui/dialogs/preferences.py
fibsem/applications/autolamella/ui/grids/__init__.py
fibsem/applications/autolamella/ui/grids/card.py
fibsem/applications/autolamella/ui/grids/overview.py
fibsem/applications/autolamella/ui/grids/protocol.py
fibsem/applications/autolamella/ui/grids/results.py
fibsem/applications/autolamella/ui/grids/run.py
fibsem/applications/autolamella/ui/grids/screen.py
fibsem/applications/autolamella/ui/grids/tab.py
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fibsem/applications/autolamella/ui/lamella/cards.py
fibsem/applications/autolamella/ui/lamella/history.py
fibsem/applications/autolamella/ui/lamella/rows.py
fibsem/applications/autolamella/ui/lamella/selected.py
fibsem/applications/autolamella/ui/lamella/tab.py
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fibsem/applications/autolamella/ui/overview/base.py
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fibsem/applications/autolamella/ui/overview/container.py
fibsem/applications/autolamella/ui/overview/fluorescence.py
fibsem/applications/autolamella/ui/panel/__init__.py
fibsem/applications/autolamella/ui/panel/experiment.py
fibsem/applications/autolamella/ui/protocol/__init__.py
fibsem/applications/autolamella/ui/protocol/dialogs.py
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fibsem/applications/autolamella/ui/protocol/forms.py
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fibsem/applications/autolamella/ui/protocol/lamella_template.py
fibsem/applications/autolamella/ui/protocol/load.py
fibsem/applications/autolamella/ui/protocol/picker.py
fibsem/applications/autolamella/ui/protocol/protocol_tab.py
fibsem/applications/autolamella/ui/workflow/__init__.py
fibsem/applications/autolamella/ui/workflow/lamella_run.py
fibsem/applications/autolamella/ui/workflow/preflight.py
fibsem/applications/autolamella/ui/workflow/tab.py
fibsem/applications/autolamella/workflows/_default_milling_config.py
fibsem/applications/autolamella/workflows/core.py
fibsem/applications/autolamella/workflows/estimate.py
fibsem/applications/autolamella/workflows/plan.py
fibsem/applications/autolamella/workflows/runs.py
fibsem/applications/autolamella/workflows/tasks/__init__.py
fibsem/applications/autolamella/workflows/tasks/acquire_fluorescence.py
fibsem/applications/autolamella/workflows/tasks/base.py
fibsem/applications/autolamella/workflows/tasks/fiducial.py
fibsem/applications/autolamella/workflows/tasks/manager.py
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fibsem/applications/autolamella/workflows/tasks/perforation.py
fibsem/applications/autolamella/workflows/tasks/polishing.py
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fibsem/applications/autolamella/workflows/tasks/select_fluorescence_position.py
fibsem/applications/autolamella/workflows/tasks/select_position.py
fibsem/applications/autolamella/workflows/tasks/setup_coincidence_milling.py
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fibsem/applications/autolamella/workflows/tasks/trench.py
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fibsem/applications/volume/__init__.py
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fibsem/applications/volume/experiment_setup.py
fibsem/applications/volume/launch.py
fibsem/applications/volume/manager.py
fibsem/applications/volume/poses.py
fibsem/applications/volume/position.py
fibsem/applications/volume/position_milling.py
fibsem/applications/volume/protocol.py
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fibsem/applications/volume/server.py
fibsem/applications/volume/tasks/__init__.py
fibsem/applications/volume/tasks/acquisition.py
fibsem/applications/volume/tasks/base.py
fibsem/applications/volume/tasks/milling.py
fibsem/applications/volume/tasks/setup.py
fibsem/applications/volume/ui/__init__.py
fibsem/applications/volume/ui/position_editor.py
fibsem/applications/volume/ui/positions_panel.py
fibsem/applications/volume/ui/positions_tab.py
fibsem/applications/volume/ui/protocol_tab.py
fibsem/applications/volume/ui/volume_milling.py
fibsem/applications/volume/ui/window.py
fibsem/autofunctions/__init__.py
fibsem/autofunctions/acb.py
fibsem/autofunctions/autofocus.py
fibsem/autofunctions/brightness_contrast.py
fibsem/autofunctions/charge_neutralisation.py
fibsem/autofunctions/gamma.py
fibsem/autofunctions/integration.py
fibsem/autofunctions/metrics.py
fibsem/autofunctions/plotting.py
fibsem/autofunctions/stacking.py
fibsem/client/__init__.py
fibsem/client/app.py
fibsem/client/control.py
fibsem/client/events.py
fibsem/client/microscope.py
fibsem/client/pairing.py
fibsem/client/remote_microscope.py
fibsem/client/tools.py
fibsem/client/transport.py
fibsem/codec/__init__.py
fibsem/codec/upgrades/__init__.py
fibsem/codec/upgrades/autofocus.py
fibsem/codec/upgrades/configuration.py
fibsem/codec/upgrades/correlation.py
fibsem/codec/upgrades/fluorescence.py
fibsem/codec/upgrades/hardware_geometry.py
fibsem/codec/upgrades/holder.py
fibsem/codec/upgrades/image_metadata.py
fibsem/codec/upgrades/milling.py
fibsem/codec/upgrades/overview.py
fibsem/codec/upgrades/pre_task_protocol.py
fibsem/codec/upgrades/protocol.py
fibsem/codec/upgrades/records.py
fibsem/config/jeol-configuration.yaml
fibsem/config/microscope-configuration.yaml
fibsem/config/odemis-configuration.yaml
fibsem/config/sim-arctis-configuration.yaml
fibsem/config/sim-iflm-configuration.yaml
fibsem/config/tescan-configuration.yaml
fibsem/config/tfs-aquilos2-configuration.yaml
fibsem/config/tfs-arctis-configuration.yaml
fibsem/config/tfs-hydra-configuration.yaml
fibsem/config/tfs-hydra-meteor-configuration.yaml
fibsem/config/fm/fm-configuration-default.yaml
fibsem/correlation/README.md
fibsem/correlation/__init__.py
fibsem/correlation/config.py
fibsem/correlation/export.py
fibsem/correlation/fit.py
fibsem/correlation/geometry.py
fibsem/correlation/history.py
fibsem/correlation/point_fit.py
fibsem/correlation/points.py
fibsem/correlation/prediction.py
fibsem/correlation/prior.py
fibsem/correlation/refractive_index.py
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fibsem/correlation/solver.py
fibsem/correlation/structures.py
fibsem/correlation/verdict.py
fibsem/correlation/data/zeta_lut.npz
fibsem/detection/__init__.py
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fibsem/detection/detection.py
fibsem/detection/utils.py
fibsem/devices/__init__.py
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fibsem/devices/chamber.py
fibsem/devices/chamber_camera.py
fibsem/devices/core.py
fibsem/devices/entries.py
fibsem/devices/errors.py
fibsem/devices/fm.py
fibsem/devices/gis.py
fibsem/devices/manipulator.py
fibsem/devices/runs.py
fibsem/devices/sample_loader.py
fibsem/devices/scanner.py
fibsem/devices/sputter_coater.py
fibsem/devices/stage.py
fibsem/devices/wire.py
fibsem/drivers/__init__.py
fibsem/drivers/registry.py
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fibsem/drivers/autoscript/connection.py
fibsem/drivers/autoscript/devices.py
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fibsem/drivers/autoscript/manipulator_calibration.py
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fibsem/drivers/demo/devices.py
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fibsem/drivers/demo/sim_scene.py
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fibsem/drivers/jeol/devices.py
fibsem/drivers/jeol/images.py
fibsem/drivers/jeol/microscope.py
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fibsem/drivers/odemis/devices.py
fibsem/drivers/odemis/images.py
fibsem/drivers/odemis/microscope.py
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fibsem/drivers/remote/__init__.py
fibsem/drivers/remote/devices.py
fibsem/drivers/remote/services.py
fibsem/drivers/tescan/__init__.py
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fibsem/drivers/tescan/devices.py
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fibsem/drivers/tescan/microscope.py
fibsem/drivers/tescan/sdk.py
fibsem/drivers/tescan/services.py
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fibsem/fm/__init__.py
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fibsem/fm/composite.py
fibsem/fm/config.py
fibsem/fm/interpolation.py
fibsem/fm/microscope.py
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fibsem/fm/progress.py
fibsem/fm/reader.py
fibsem/fm/remote.py
fibsem/fm/reprojection.py
fibsem/fm/sem_to_fm.py
fibsem/fm/stack_file.py
fibsem/fm/structures.py
fibsem/fm/timing.py
fibsem/fm/calibration/__init__.py
fibsem/gateway/__init__.py
fibsem/gateway/__main__.py
fibsem/gateway/agent.py
fibsem/gateway/child.py
fibsem/gateway/gateway.py
fibsem/gateway/host.py
fibsem/gateway/launch.py
fibsem/gateway/main.py
fibsem/gateway/server.py
fibsem/gateway/ui/__init__.py
fibsem/gateway/ui/tray.py
fibsem/geometry/__init__.py
fibsem/geometry/angles.py
fibsem/geometry/frames.py
fibsem/geometry/movement.py
fibsem/geometry/orientations.py
fibsem/geometry/projection.py
fibsem/geometry/saved_images.py
fibsem/geometry/similarity.py
fibsem/geometry/stage_places.py
fibsem/imaging/__init__.py
fibsem/imaging/analysis.py
fibsem/imaging/animation.py
fibsem/imaging/cells.py
fibsem/imaging/drawing.py
fibsem/imaging/export.py
fibsem/imaging/labels.py
fibsem/imaging/latest.py
fibsem/imaging/localise.py
fibsem/imaging/looks.py
fibsem/imaging/marks.py
fibsem/imaging/masks.py
fibsem/imaging/overview_session.py
fibsem/imaging/reduce.py
fibsem/imaging/spot.py
fibsem/imaging/thickness.py
fibsem/imaging/thumbnail.py
fibsem/imaging/tiled.py
fibsem/imaging/utils.py
fibsem/imaging/tiling/__init__.py
fibsem/imaging/tiling/geometry.py
fibsem/imaging/tiling/layout_check.py
fibsem/imaging/tiling/plotting.py
fibsem/imaging/tiling/progress.py
fibsem/imaging/tiling/reach.py
fibsem/imaging/tiling/registration.py
fibsem/imaging/tiling/reprojection.py
fibsem/imaging/tiling/result.py
fibsem/milling/__init__.py
fibsem/milling/base.py
fibsem/milling/config.py
fibsem/milling/core.py
fibsem/milling/monitor_config.py
fibsem/milling/progress.py
fibsem/milling/properties.py
fibsem/milling/readings.py
fibsem/milling/rtm.py
fibsem/milling/steps.py
fibsem/milling/tasks.py
fibsem/milling/monitors/__init__.py
fibsem/milling/monitors/base.py
fibsem/milling/monitors/fm_intensity.py
fibsem/milling/monitors/intensity.py
fibsem/milling/monitors/rtm.py
fibsem/milling/monitors/sem_peek.py
fibsem/milling/patterning/__init__.py
fibsem/milling/patterning/base.py
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web/.gitignore
web/bun.lock
web/components.json
web/index.html
web/package.json
web/tsconfig.json
web/vite.config.ts
web/src/App.tsx
web/src/index.css
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web/src/components/layers-panel.tsx
web/src/components/mark-for-agent.tsx
web/src/components/marks.tsx
web/src/components/stage-card.tsx
web/src/components/stepper.tsx
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web/src/components/ui/button.tsx
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web/src/components/ui/dialog.tsx
web/src/components/ui/hover-card.tsx
web/src/components/ui/popup.tsx
web/src/lib/api.ts
web/src/lib/eventText.ts
web/src/lib/events.ts
web/src/lib/experiment.ts
web/src/lib/files.ts
web/src/lib/format.ts
web/src/lib/gl-layers.ts
web/src/lib/layers.ts
web/src/lib/markdown.tsx
web/src/lib/marks.ts
web/src/lib/notify.ts
web/src/lib/planes.ts
web/src/lib/route.ts
web/src/lib/types.ts
web/src/lib/utils.ts
web/src/pages/Agent.tsx
web/src/pages/Events.tsx
web/src/pages/Experiment.tsx
web/src/pages/Gateway.tsx
web/src/pages/Grids.tsx
web/src/pages/Lamellae.tsx
web/src/pages/Microscope.tsx
web/src/pages/Positions.tsx
web/src/pages/agent/Attachments.tsx
web/src/pages/agent/Cards.tsx
web/src/pages/agent/Composer.tsx
web/src/pages/agent/Customisation.tsx
web/src/pages/agent/Knowledge.tsx
web/src/pages/agent/Knowledge.tsx.orig
web/src/pages/agent/Library.tsx
web/src/pages/agent/Picker.tsx
web/src/pages/agent/Pictures.tsx
web/src/pages/agent/PlanDialog.tsx
web/src/pages/agent/Settings.tsx
web/src/pages/agent/SidePanel.tsx
web/src/pages/agent/SidePanel.tsx.orig
web/src/pages/agent/act.ts
web/src/pages/agent/attach.ts
web/src/pages/experiment/Replay.tsx
web/src/pages/gateway/AgentCard.tsx
web/src/pages/lamellae/History.tsx
web/src/pages/lamellae/ItemList.tsx
web/src/pages/positions/Scrubber.tsx
web/src/shell/AgentChip.tsx
web/src/shell/Notices.tsx
web/src/shell/Pair.tsx
web/src/shell/Rail.tsx
web/src/shell/Settings.tsx
web/src/shell/TopLine.tsx