SegViewer

A python-based GUI that visualises image and matching segmentation mask side-by-side

Installation

No installation required. Just clone github repository.

Manual

1. Execute pairviewer.py in your terminal:

python ./pairviewer.py

2. Use the Select file button to open a .csv file containing paths to pairs of images (see example_list.csv). Format example:

/path/to/image/1a.png	/path/to/image/1b.png
/path/to/image/2a.png	/path/to/image/2b.png
/path/to/image/3a.png	/path/to/image/3b.png
...	...

Note: For Schroeder Lab movies use 8bit movies with well-set black-point and white-point for good contrast images.


3. Binarize intensities of the left or the right frame using the checkbox below the frames.

4. Enhance the contrast of the left or the right frame using the checkbox below the frames.

5. Navigate through image pairs using left (←) and right (→) arrow on your keyboard

6. Image pairs can be marked using upward (↑) arrow on your keyboard. Marked image pairs are highlighted by a red border and the index of marked image pairs will be denoted in the list on the right. To unmark a marked pair of images, use the downward (↓) arrow on your keyboard.

7. The list of marked images can be saved (same format as in 2.) to a .csv file using the Save list button.

Note: When saving a file do not enter the file suffix. It will be added automatically.
Note2: Save a list after marking an image. Step 9. will allow you to continue where you left off.


8. Continue working on an existing list of marked images using the Load list button.

Note: Loading a list of marked images requires loaded image pairs (see 2.).


9. Use the Go to position button to move between marked pairs. Select the position you want to move to in the list on the right and click Go to position.

ToDo

• everything perfect