ThioBac Tester

A test macro for curvature evaluation along cell perimeter

N.Vischer, 16-Dec-2016

These two videos show how to test and quantify longitudinal cell division.
The ThioBac Tester runs with or without ObjectJ:
Movie ThioBac Tester (90 sec)

The ThioBac Project shows suggetions for automated analysis with ObjectJ:
Movie ThioBac Project (2:55 min)

Download


Fig 1:
Tool:
- Tool bar shows TestTool (TT icon)
Image (right)::
- Clicking cell with Test tool starts shape analysis

Plot window:
- Radius vs perimeter position (red),
- Curvature vs perimeter position (blue),
- Shaded green and blue test areas correspond to perimeter colors
- If curvature goes below yellow threshold, an invagination is marked.
- Vertical red cursor bar appears at click position

Box window:
- Enlarged object with contour (magenta)
- Green sensing contour for 'Upper' pole (here: left)
- Blue sensing contour for 'Lower' pole (here: right)
- Polar invaginations (here: two are found) are indicated with a point
- Small red circle shows perimeter point when clicking in the plot window.-


Fig 2:
Searching for deep invagination
A sensor line (yellow) starts at the polar invagination. As long as its intensity profile shows a maximum (=beginning cell division), the sensor line is moved towards the cell center.
Overlay Elements:
You can activate any of the ROIs by double-clicking it in "Overlay Elements". Here, the third sensor line "sensorU3" is selected. 'U' stands for 'upper' (=green pole), and 'L' stands for 'lower' (=blue pole).


Fig 3:
Searching for deep invagination
Double-click the "TT" tool to adjust bending threhold, and choose which type of deep invagination should be shown.


Try out:

Additional macros are just there to create single key shortcuts:
- ThioBac Tool Options [1]"
for changing curvature threshold and visibility of depth sensors
- Change LUT [2]
Steps through gray, Fire, Inverted Fire Lookup table
- List Elements [3]
A hortcut to list overlay elements; double-click a row in the table to select that ROI