Pointing cell Tracking



Lucas Santiago Palacios Ruiz, IBEC, Barcelona (Spain).



2015/08/25: First version


ImageJ 1.34k or later




Download Pointing_cell_tracking.jar and install it from plug-in menu.


This plug-in is a fork of Manual Tracking which has been improved in order to collect the position information of objects without clicking. Just point with your mouse while images are automatically passing and you will track object positions. Furthermore, it has been added some graphic new options. To see all what original plugin could make, please see documentation in pdf format. The added enhancements are now displayed:




As in Manual Tracking, in order to start tracking you have to click “Add track”. Then, you only have to click once over the object you want to track and imageJ will automatically pass every photo of your stack. Photos will change every X ms, where X is the number that you can change in “Automatic field” (by defect 100 ms, that is, 10 photos/s). Depending on your object, 3 possibilities could happen:

·         Your object is present all time story. Just follow it with your mouse. When the stack is over you can add a new track pressing on “Add track”.

·         Your object is present from the beginning to some middle time point. Follow your object with your mouse and when it disappears, click over the image with the middle button of your mouse (the wheel button). Then, press “End track”. You can now add a new track pressing on “Add track”.

·         Your object is present from some middle time point to another time point/end.  Put your mouse over the image and when your object appears click over the image with the middle button of your mouse (the wheel button). Then, press F8 button from the keyboard to erase older positions tracked. It is important to have selected the image in order to do the delete. If you cannot see the list of tracks, press F5 button from the keyboard. When you are sure that older tracks positions have been deleted, click again over the image with the middle button to follow the tracking. If your object disappears before the end of the stack, click with the middle button of your mouse and the click “End track”. In any case, press “Add track” if you want to add a new track after this tracking.


To sum up:

·         Wheel button mouse. Stop/Resume tracking. You need to press this button if you want to click F8 or F5.

·         F5: Show track list.

·         F8: Erase older tracks from the current object.


Figure 1:




In many cases, you will notice that in older Manual tracking versions when you press any button from drawing, imageJ (and probably your pc too) started to slow down its velocity and eventually it freezes. This is because when any of these buttons are pressed, ImageJ creates a new image that is stored in your RAM and sometimes this fills your entire RAM available. For example, a stack of 290 photos (1344x1024 px²) in 8-bit costs around 390 MB of RAM and if you press “Dots” it will create you a new RGB image of 1.5 GB. In order to solve this problem now you can do:

·         Create the same video but in 8-bit color. In this case, you have to activate “All same color”. All dots/lines will be painted with the same color as the field next to “All same color” and it must be a number between 0 (black) and 255 (white). In the previous example, the new video will cost ~390 MB in comparison to 1.5 GB.

·         Create only the first image. In this case, you have to activate “Only first”. This option should be done with dots only. It will paint all first objects positions tracked either if its track start at frame 1 or in other frame. If “All same color” is checked, the image created will be in black and white. Nevertheless, you could create it in color without fear because following with the example, it would be ~ 5 MB.

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