Quick Annotation Tool Module Guide

The Quick Annotation Tool is a browser-based painting interface for creating ground-truth segmentation masks on TIFF image stacks. These annotations serve as training data for U-Net segmentation models or can be used directly for mesh generation.

For a conceptual overview, see Annotation.

The Annotation Tool module landing page showing step navigation and file selector

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Quick Start

1. Launch module — Click "Quick Annotation Tool" from the workspace hub
2. Select an image — Choose a TIFF stack to annotate (new, resume, or edit)
3. Paint annotations — Use the brush tool to label regions of interest
4. Navigate slices — Use arrow keys or buttons to move through the stack
5. Save your work — Click "Save Progress" or "Create Annotation" when done

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Step-by-Step Guide

Step 1: Data Selection

Choose your source image and annotation mode.

Step 1 with annotation mode selection and file chooser

Input Options

Mode	Description	When to Use
New Annotation	Start fresh on a raw TIFF image	Creating annotations from scratch
Resume	Continue an unfinished annotation	Returning to work in progress
Edit	Modify an existing completed annotation	Refining previous work

File Requirements

• Format: Multi-page TIFF (.tif or .tiff)
• Bit Depth: 8-bit or 16-bit grayscale
• Channels: Single channel (grayscale)

Tip: Large files work but may affect performance. Consider splitting very large stacks.

Note (Resume/Edit): both modes need the original image behind the annotation. The tool finds it automatically through the file's lineage; when it can't (an uploaded mask with no lineage, or a deleted source), a picker appears — the image you pick must match the annotation's width, height, and slice count.

For more details, see Source Image.

Click "Next" to proceed to the annotation interface.

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Step 2: Annotation Interface

The annotation interface provides all tools needed to paint segmentation masks.

Annotation interface with canvas, toolbar, and control areas

Interface Layout

Area	Location	Purpose
Canvas	Center	Main painting area showing current slice
Toolbar	Right side	Tools, brush size, history, and class management
Control Bar	Above canvas	Slice navigation and zoom controls
Status Bar	Below canvas	Cursor coordinates and image dimensions

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Tools

Brush Tool

Paint annotations with the currently selected class.

Property	Value
Shortcut	B
Behavior	Click and drag to paint continuous strokes
Color	Uses the active class color

Eraser Tool

Remove annotations by painting with background (transparent).

Property	Value
Shortcut	E
Behavior	Click and drag to erase
Effect	Sets pixels to background (class 0)

Tip: The eraser respects class visibility—it only erases classes that are currently visible.

For more details, see Annotation Tools.

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Brush Size

Control the size of your brush and eraser.

Brush size slider in the toolbar with pixel size display

Control	Action
Slider	Drag to adjust size (1-50 pixels)
[ key	Decrease size by 5 pixels
] key	Increase size by 5 pixels

The current size is displayed next to the slider (e.g., "10px").

For more details, see Brush Size.

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Class Management

Manage the classes (labels) you're annotating.

Class management panel with color swatches and visibility toggles

Class List

Each class shows:

• Color swatch — The class color (auto-assigned)
• Name — Class label (e.g., "Class 1")
• Visibility toggle — Show/hide this class on canvas
• Delete button — Remove class and all its pixels

Class Actions

Action	How
Add class	Click the "+" button in the Classes header
Select class	Click on a class to make it active for painting
Toggle visibility	Click the eye icon to show/hide
Delete class	Click the × button (removes all pixels with that class)

Note: Colors are automatically assigned using a color distribution algorithm that ensures good visual separation between classes.

For more details, see Annotation Classes.

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Canvas Controls

Zoom

Control	Action
+ button	Zoom in (125% of current)
− button	Zoom out (80% of current)
Fit button (⊡)	Auto-fit image to view
1:1 button	Reset to 100% zoom
Mouse wheel	Scroll to zoom (toward cursor)

Zoom range: 10% to 1000%

Pan

Method	How
Right-click + drag	Pan the canvas
Middle-click + drag	Pan the canvas
Space + left-click + drag	Hold Space, then drag to pan

Tip: When zoomed in, the cursor changes to a hand icon to indicate you can pan.

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Slice Navigation

Navigate through the 3D stack to annotate each slice.

Slice navigation with previous/next buttons and position indicator

Control	Action
◀ button	Go to previous slice
▶ button	Go to next slice
Left arrow key	Previous slice
Right arrow key	Next slice
Slice indicator	Shows current position (e.g., "12 / 64")

Note: Each slice has its own independent undo/redo history.

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History (Undo/Redo)

Undo and redo your painting actions on the current slice.

Action	Shortcut	Button
Undo	Ctrl+Z (Cmd+Z on Mac)	↶ button
Redo	Ctrl+Y or Ctrl+Shift+Z	↷ button

• History is per-slice — each slice maintains its own history
• Maximum 20 undo states per slice
• Buttons are disabled when no history is available

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Saving Your Work

Both save actions become available after your first stroke.

Save Progress

Save your work-in-progress (WIP) to continue later.

• Button: "Save Progress" (in header)
• Resume: the WIP file appears under "Unfinished annotations" in Step 1's source selector; further saves keep updating the same file

Create Annotation

Finalize your annotation for use in training or mesh generation.

• Button: "Create Annotation" (in header)
• Use: ready for Segmentation training, Segmentation Cleanup, or Mesh generation
• If no pixels have been painted, a confirmation is asked before creating an empty annotation
• In Edit mode, saving never overwrites the original — it creates a new file

Note: leaving the module or closing the tab with unsaved changes asks for confirmation first.

Autosave

Automatic saving protects against data loss.

Setting	Default
Enabled	Yes (toggle in toolbar)
Interval	Every 2 minutes
Condition	Only saves if changes exist

Tip: Even with autosave enabled, remember to click "Create Annotation" when you're finished to mark the annotation as complete.

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Keyboard Shortcuts

Shortcut	Action
B	Switch to brush tool
E	Switch to eraser tool
[	Decrease brush size
]	Increase brush size
Ctrl+Z	Undo
Ctrl+Y	Redo
Left Arrow	Previous slice
Right Arrow	Next slice
Space + Drag	Pan canvas
Mouse Wheel	Zoom in/out

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Output Files

File	Description
Final annotation	Multi-page TIFF with class labels as pixel values, tagged as an annotation — accepted by Segmentation, Segmentation Cleanup, Mesh Generation, and Stitching
Work-in-progress file	Saved by "Save Progress"/autosave; listed under "Unfinished annotations" in Step 1

TIFF Format:

• 8-bit grayscale
• Pixel value = class ID (0 = background, 1+ = classes)
• One page per slice in the stack

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Troubleshooting

Issue	Cause	Solution
Can't paint on canvas	Wrong tool or no class selected	Press B for brush, ensure a class is selected
Brush not visible	Class visibility turned off	Click the eye icon to show the active class
Undo not working	No actions to undo on this slice	Undo history is per-slice; may need to check other slices
Changes not saving	Network error or autosave disabled	Click "Save Progress" manually; check console for errors
Image not loading	File too large or invalid format	Try a smaller file or check TIFF format
Lost my work	Browser closed without saving	Check "Unfinished annotations" in Step 1 for autosaved progress

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Related Help Articles

Module Overview:

• Quick Annotation Tool — Module introduction and concepts

Tools & Controls:

• Drawing Tools — Brush and eraser details
• Brush Size — Size adjustment and shortcuts
• Annotation Classes — Adding and managing classes
• History & Autosave — Undo/redo and automatic saving

Data:

• Source Image Selection — Input requirements