arayoshipta / SimplePTA

#SimplePTA

About

SimplePTA is a ImageJ1.x plugin that enable semi-automatic object tracking.

Important

This plugin is free to use, but the copyright is not abandoned. I HAVE NO RESPONSIBILITY TO ANY DAMAGE BECAUSE OF THE USE OF THIS PLUG-IN

##Install If you are beginner, I recommend you to use Fiji since it equips all required libraries for SimpltPTA.

Fiji

1. Put "SimplePTA_.jar" in jar folder into Fiji's plugins folder
2. Start Fiji, then you'll find "SimplePTA" in plugins menu bar

ImageJ

1. Download additional jar files as follows

• JFreeChart.jar
• JCommons.jar
  • These can be downloads from JFreeChart
• commons-math3-3.x.x.jar
  • Apache Commons Math

Usage

Multiple tracking

1. Prepare stack image.
2. Launch SimplePTA from plugin menu.
3. Adjust threshold. This process is required if you want to store Size information.
4. Choose tracking methods from Main Window. Now I offer "Centroid", "Center of Mass", and "2-Dimensional Gaussian Fitting"
5. Click object what you want to track. The cross-target will appear.
6. Press "Single Track" button to perform tracking.
7. After tracking cells, Result table data will appear.

Table

1. When you click the row of table, multi-plot graph will be appeared.
2. Multiple selection enables multiple indication of Roi's in the image.
3. Table has tow menus, Save and Edit

Save menu

1. You can save your data as text data from save menu.
   • I encourage you to analyze data by Pandas in python.

Edit menu

1. You can delete, split, and concatenate tracks.
2. Split can be performed at the current frame
3. To concatenate tracks, choose two tracks that don't overlap about time.
4. If there is a gap between last frame of first track and first frame of second track, simple interpolation will be performed.

History

• 2016.08.01 version 0.5 was uploaded
• 2017.01.12 version 0.7.1 was uploaded

Author information

Yoshiyuki Arai

E-mail: [e-mail]