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# The Annotations Tool

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## Overview

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

- MIB in brief: Annotations
- MIB in brief: Annotations

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

- 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 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 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

- 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:

- 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

Back to MIB | User interface | Panels | Segmentation