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The Annotations Tool

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Overview

Annotations Tool

Tools to add/remove annotations, marking specific locations with labels and values.

Addition and removal of annotations
  • : add an annotation at the mouse cursor.
  • Ctrl + : remove the closest annotation.
  • Shift + : interpolate annotations between the previous and new annotation across dataset depth.

Annotation panel widgets

  • Annotation list open a window listing annotations. Load/save to MATLAB workspace or file (MATLAB/Excel formats), see below.
  • Delete All remove all annotations.
  • Precision specify digits after the decimal point.
  • Show prompt show a dialog for label/value after adding an annotation; otherwise, use the previous annotation’s values.
  • Focus on Value prioritize value over label during visualization.
  • Display as: choose display mode in the Image View panel:
    • Marker: show only a cross-marker.
    • Label: show marker and label.
    • Value: show marker and value.
    • Label + Value: show marker, label, and value.

List of annotations

Annotations Table

  • List of annotations table: shows annotations.
Right-click () for options
  • Jump to annotation: center the selected annotation in the Image View panel.
  • Add annotation: manually add an annotation by manually specifying its position, value and name.
  • Rename selected annotations: rename selected annotations.
  • Batch modify selected annotations: modify values/coordinates with expressions (e.g., set, multiply, add).
  • Count selected annotations: count occurrences, displayed in MATLAB and copied to clipboard. Demo
  • Copy selected annotations to clipboard: copy as text for Excel.

  • Paste from clipboard to column: paste Excel values to a selected column.

  • Convert to Mask Convert selected annotations to Mask: generate 2D/3D Mask spots from annotations (fixed or scaled size).

  • Crop out patches around selected annotations: generate 2D/3D patches with customizable options (e.g., jitter). Demo
  • Interpolate annotations across slices Interpolate between selected annotations: interpolate annotations across slices (linear for two, linear/cubic/spline for more).

  • Export selected annotations:

    • export to MATLAB
    • Amira landmarks (coordinates only)
    • PSI format
    • Excel

  • Export selected annotations to Imaris: export to Imaris (export dataset first).

  • Order: move annotations up/down the list.
  • Delete annotation: delete selected annotations.

Tools panel

Convert to Mask

  • Load import annotations from MATLAB or a file.
  • Save export to MATLAB, CSV, Excel, Amira landmarks (coordinates only), or PSI format. Demo
  • Precision adjust value field precision.
  • Auto jump center the selected annotation in the Image View panel.
  • Sort table sort by Name, Value, X, Y, Z, T.
  • Settings:

Annotations visualization settings

  • Show annotations for extra slices: set depth range (0 = current slice only).
  • Annotation size: set marker size (8–20pt).
  • Annotation color: select color.
  • Refresh table update the list.
  • Delete all remove all annotations.

Presets

Use the following key shortcuts to define and restore presets

  • Shift+1, Shift+2, Shift+3 - store preset 1, 2, or 3 correspondingly
  • 1, 2, 3 - restore preset 1, 2, or 3 correspondingly

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