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The Annotations Tool

BigData mode: supported

Annotations work with BigData datasets (they are stored as coordinates, independent of resolution).

Overview

Annotations Tool

Tools to add/remove annotations, marking specific locations with a label and a value.

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.
  • 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.
  • Delete All remove all annotations.
  • 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.

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

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). Annotations Table
  • 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
Crop patches dialog

Convert to Mask

Each patch is centred on an annotation coordinate. The dialog controls how large the patches are, where they go, and what layers are included.

Output destination

  • Crop to file — saves each patch as a separate image file in the chosen directory. Supported formats: TIF (LZW or uncompressed), Amira Mesh binary (*.am), MRC for IMOD (*.mrc), NRRD (*.nrrd).
  • Crop to MATLAB — exports each patch as a struct into the MATLAB workspace under an auto-generated variable name. The struct contains img (pixel data), pixSize (voxel size), and optionally Model and Mask subfields.

Patch dimensions

  • Width, px — total patch width in pixels (centred on the annotation X coordinate).
  • Height, px — total patch height in pixels (centred on the annotation Y coordinate).
  • Crop 3D objects checkbox — when checked, crops a 3D slab; the Depth field sets the number of slices centred on the annotation Z coordinate.

Filename options (file output only)

A dialog asks which components to append to the base filename:

  • annotation name
  • Z, X, or Y coordinate
  • slice name as the filename template (uses per-slice names from the dataset when available)

Include model / mask

  • Crop Model — include a cropped copy of the model layer alongside each image patch; choose the save format from the adjacent dropdown.
  • Crop Mask — include a cropped copy of the mask layer; choose its format separately.

Jitter

Adds a random XY offset to each patch centre, useful for data augmentation:

  • Variation — maximum pixel offset in each direction (offset drawn from ±Variation).
  • Seed — random seed for reproducibility; 0 uses a new random seed each run.
  • 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 selected annotation(s): 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.

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