Annotation Workflow

Annotation Workflow

This page explains how to annotate cells, manage keyframes, and assign samples.

Choose the right mode

Use the cursor tool when you need to:

• select cells
• inspect cells
• edit freeze frames
• assign samples

Use the add or grid tools when you need to:

• place one cell at a time
• lay out many cells quickly in a regular pattern

Use edit modes when you need to:

• correct an existing placement
• refine a group
• update a keyframed layout

Add one cell

Use single-cell placement when:

• the layout is irregular
• the number of cells is small
• you need exact manual control

Typical workflow:

1. Activate the single-cell tool.
2. Set the radius in the tool options or status bar.
3. Click the center of the droplet or well.
4. Repeat for the remaining cells.

Add a grid

Use grid placement when:

• droplets or wells follow a regular pattern
• row and column counts are known
• you want faster initial placement

Typical workflow:

1. Activate the grid tool.
2. Set rows, columns, horizontal pitch, vertical pitch, and rotation.
3. Position the preview over the image.
4. Commit the grid once it matches the array.

Edit existing cells

Use edit mode to correct:

• position
• radius
• grid pitch
• grid rotation

The main rule is to edit the minimum number of frames necessary. If the layout only changes at certain points in the run, use keyframes instead of manually fixing every frame.

Use keyframes when cells move

Keyframes are the main way to manage motion across a sequence.

Use them when:

• the field drifts
• the camera or stage shifts
• the array geometry changes across time

The intended workflow is:

1. mark a keyframe at a frame with a known good layout
2. adjust cells there
3. add another keyframe later if the layout changes again

Icescopy interpolates between keyframes.

This is why the app uses a global keyframe model instead of per-cell tracks. The motion source is usually global drift, not an independent animation per cell.

Use flags during review

Flags are review markers. They are useful when:

• you want to revisit a frame
• you see an ambiguous event
• you want to compare a frame during QC

Flags do not change analysis by themselves.

Delete cells

Delete only when the ROI is truly wrong or no longer needed.

If you only need to correct a position:

• edit it
• do not delete and recreate it unless the ID continuity no longer matters

Edit freeze frames

Freeze frames can be corrected manually from the cursor/inspection workflow.

Use that when:

• the automatic detector missed a real event
• the automatic detector chose the wrong frame
• a special case needs a manual override

Assign samples

Assign samples when the array contains multiple experimental groups.

Sample assignment affects:

• grouped output summaries
• temperature import grouping
• interpretation of results tables

Use the sample catalog

The sample catalog gives names to sample IDs.

Use it to keep exports readable and to avoid treating numeric sample IDs as the only user-facing identifiers.

Use the cells panel

The cells panel is the structural summary of current annotation state.

Use it to review:

• which cells exist
• which sample each cell belongs to
• which freeze frames are assigned

Recommended order

Use this order for the least rework:

1. place cells
2. correct geometry
3. add keyframes if the layout moves
4. assign samples
5. review freeze frames only after analysis has been run