How-to: using ROI

A step-by-step guide on how to use Napari-Correct-Drift on one 2D movie.

The movie shows an growing root tip from vertical microscopy. The object is moviing, while the background is constant. This requires us to use a regions-of-interest (ROI) to focus the correction on the root object. For the rest we will only use default parameters.

0. Download sample movie

Click on root tip and save the root_2.tif` file.

1. Open Napari and load movie

In Napari: File->Open Files(s) and select movie

You should see:

2. Open Napari-Correct-Drift plug-in

In Napari: select Plugins->Napari Correct Drift (napari-correct-drift) from menu

Napari viewer with Napari-Correct-Drift widget on the right

3. Check the Use ROI checkbox

In the Napari-Correct-Drift widget on the right, activate the the Use ROI checkbox. This will add a new shape layer called ROI

4. Draw rectangular ROI over root

Choose rectangular ROI and draw onto image

5. Estimate drift

Estimate drift by clicking the Estimate drift button in the Napari-Correct-Drift widget.

This will bring up the drift table widget (lower right) after ~10 seconds.

6. Correct drift

Correct drift by clicking the Correct drift button in the Napari-Correct-Drift widget.

This will add another image shape layer root_2 (corrected)

Now you can inspect the correction result by using the time slider, i. e. Axis 0