Using the GUI#

Once the application is running (see Running the GUI), you can start a new annotation session or load an existing one.

The application organizes annotations using two levels:

  • Images: a session can contain multiple images.

  • Groups: each image can contain annotations belonging to several groups.

Images management#

Images are managed from the Images panel.

To add images, click on the “+” button and select one or multiple image files. Each image is loaded into the current session and receives its own annotation manager.

Multiple images can be loaded at the same time:

image_1.png
image_2.png
image_3.png

The image selector allows switching between all loaded images.

Note

Image paths containing commas (,) are not supported because commas are used as separators in the CSV session format.

To remove the current image, click on the trash button. Removing an image permanently removes all annotations associated with it.

Groups management#

Annotations are organized into groups shared by all images.

To manage groups:

  • Add a group: Click on the “+” button in the Groups panel and enter a group name.

  • Rename a group: Select a group and click the rename button.

  • Delete a group: Select a group and click the trash button.

  • Switch groups: Use the group selector to change the active annotation group.

New clicks are always added to the currently selected image and group.

Adding Clicks#

Annotations are created directly on the displayed image.

  • Left click: Add a point at the clicked position.

  • Right click: Add an empty point (None, None).

Empty points can be used when a click is intentionally skipped while keeping the annotation order.

Coordinates are stored internally as floating-point values.

The coordinates follow NumPy indexing conventions:

image[y, x]

where:

  • x is the horizontal coordinate (column),

  • y is the vertical coordinate (row).

Coordinate system#

By default, pixel coordinates use the center of the first pixel as the reference point:

(0, 0)

The Half-shift coordinates option changes this convention by shifting coordinates by 0.5.

All coordinates remain stored as floating-point values. The display format in the table can be changed using the Integer precision option.

Image navigation and display#

The image viewer supports:

  • Mouse wheel: Zoom in and out.

  • Middle mouse button drag: Move the image while keeping the button pressed.

The display panel allows changing:

  • contrast,

  • colormap,

  • marker appearance,

  • click visibility.

Removing clicks#

To remove annotations:

  • Undo: Removes the last click from the current image and group.

  • Clear: Removes all clicks from the current image and group.

Saving and loading sessions#

A complete annotation session can be saved as a CSV file.

A session contains:

  • all image paths,

  • all groups,

  • all annotation points.

To save a session:

  1. Click Save Session CSV.

  2. Choose the output .csv file.

The generated CSV format is:

Image,Group,Index,X,Y
image_1.png,default,0,276.5,97.0
image_1.png,default,1,242.2,109.8
image_2.png,target,0,317.0,144.5

Empty clicks are stored as empty coordinates:

Image,Group,Index,X,Y
image_1.png,default,2,,

To restore a previous annotation session:

  1. Click Load Session CSV.

  2. Select the session file.

The current session will be replaced by the loaded session.

Keyboard shortcuts#

The following shortcuts are available:

Shortcut

Action

Ctrl+O

Add image(s)

Ctrl+Shift+O

Load annotation session

Ctrl+S

Save annotation session

Ctrl+Z

Remove last click

Ctrl+Shift+Z

Remove all clicks from current image/group

Ctrl+G

Create a new group

F2

Rename current group

Ctrl+Q

Quit application

F1

Open help

Space

Toggle click display

Ctrl+Right // N

Switch to next image

Ctrl+Left // P

Switch to previous image

Ctrl+Down

Switch to next group

Ctrl+Up

Switch to previous group