Drift Corrector User Guide

This document is a user guide for the Drift Corrector toolbox for performing correctional translation of isotropic images with visible vesicles.

The general process includes

1. Open a dataset to be corrected (we currently support a number image, including multipage tiff images or a numbered image files in various formats such as TIF, PNG, JPG, and BMP).
2. Annotate vesicles individually until the target error becomes low enough found for each image section.
3. Generate a corrected dataset.

The process requires a few manual steps which are covered here in detail.

Open a dataset

1. To open a dataset, make sure it is in a supported format. If stored as multiple image files, place these in a separate folder with names ending by a number (e.g., my_image_01.png, my_image_02.png, ...) starting at either 0 or 1, numbered consecutively. Additionally, multipage TIF files are also supported.

   

2. To open the dataset, click Open Dataset in the left pane. When prompted, choose the dataset format.

   

3. Navigate to the dataset.

   

4. Large datasets may take a moment to load.

   

Save Annotation Progress

Saving progress is done automatically in a automatically created subdirectory inside the datasets directory and does not require actions by the user.

Annotate a vesicle

1. Ensure Add Points mode is enabled in the left pane.

   

2. Use mouse scroll to navigate the image sections if needed.

   

3. Right-click a vesicle to pan to it.

   

4. Zoom in a size where accurate annotation is possible.

   

5. Left-click a vesicle boundary to annotate a point.

   

6. Use mouse scroll to navigate the image sections to annotate the vesicle across multiple sections.

   

7. Click the "a" button to change viewing and annotation axis. When not viewing in the standard image plane, the right pane shows statistics on the predicted accuracy of the drift estimate. In the standard view, this pane shows details about the current section.

   

8. To delete a point, ensure the Edit Points mode is enabled. Left-click the point to delete it.

   

9. When done annotating the vesicle, click Next Vesicle in the left pane. Notice the changes in the right pane. The confidence interval (green line) and vesicle count (black line) changes to reflect a drift estimate with the new vesicle annotated.

   

Edit an annotated vesicle

1. Ensure Edit Points is selected in the left pane.

   

2. Right-click a vesicle to activate it for editing points.

   

3. In Edit Points mode, left-click to delete points.

   

4. In Add Points mode, left-click to add points.

   

5. When done annotating the vesicle, click Next Vesicle in the left pane.

   

Save corrected dataset

1. It is recommended first to create a folder to contain the corrected dataset.

2. Click Save Corrected Dataset in the left pane. Choose an output format and click submit.

   

3. Navigate to a target directory for the output. Warning: Choosing a directory containing other files may overwrite the existing data.. When done, click OK.

   

4. Wait while the corrected dataset is produced.

   

5. The output dataset is extended in size so that no parts of the dataset is transformed outside the view.