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manually align specimens to annotated 3D spaces
C++ Python CMake
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README.md

CellLocator by Allen Institute

Manually align specimens to annotated 3D spaces

CellLocator by Allen Institute

Keyboard Accelerators and Mouse Operations

On macOS use the Command key (⌘) instead of the Control (Ctrl) key

General

Key Effect
Ctrl + n Create a new annotation
Ctrl + s Save current annotation
Ctrl + o Load an annotation from file
Ctrl + w Reset views discarding current changes

If it applies, user will be prompted with a save dialog before creating, saving or loading a annotation.

2D Viewer

Key Effect
f Increment Slice offset
b Decrement Slice offset
r Adjust field of view to match the extent of the atlas

Zoom and Pan (available in Exploration and Edit mode)

Interface Device Zoom Pan
3-button mouse Right-Click & vertical drag Middle-Click & drag
2-button mouse Right-Click & vertical drag Shift+Left-Click & drag
1-button mouse Ctrl+Left-Click & vertical drag Shift+Left-Click & drag
Trackpad two-fingers & vertical drag Shift+Left-Click & drag

Annotation (available in Edit mode)

Key or mouse operation Effect
Left-Click Add annotation point
Delete Delete currently selected annotation point
Ctrl + Left-Click on annotation line Insert annotation point
Left-Click near annotation line & drag Translate annotation
Right-Click near annotation line & drag Scale annotation

3D Viewer

Key Effect
f Increment Slice offset
b Decrement Slice offset
r Adjust field of view to match the extent of the atlas

SpinBoxes and Sliders

  • Right/Left key: SingleStep increment
  • PageUp/PageDown key: PageStep increment
SingleStep increment PageStep increment
Raw/Pitch/Yaw 1 5
Annotation Thickness 1 10
Slice Step Size 1 10
Slice Offset <slice step size> <slice step size> * 10

Known Issues

  • Inserting point in a Spline annotation does not work reliably. Workaround by switch the annotation type to PolyLine and then inserting the point. See #80
  • For Roll, pitch and yaw, the angle mappings differ from the coordinate system the lab uses. See #81
  • After using Ctrl+w and restarting the application, mm unit prefix is displayed instead of um. See #89
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