WhatToDo.txt

CellTraxx INSTRUCTIONS

To run CellTraxx, see the user manual. The preparation procedure includes copying the entire folder "celltraxx_system" to the root of the local C drive such that its path becomes "C:\celltraxx_system\". 

Make a new folder "C:\celltraxx_data\" and copy the below mentioned videos in sequence into this data folder. 

Two example video files are given in the folder "Example_videos_for_testing". Due to their large size, they are stored on Dropbox and can be accessed through the link  
https://www.dropbox.com/sh/uwv0cmwapfsgasp/AAAe_hj-UQ9YvQNVozu0puW6a?dl=0 

The two example videos are: 

1_Random_migration_HeLa_cells.avi
Migrating HeLa cells captured every 10 minutes for 14 hours in Incucyte S3. Pixel size 1.24 µm. 

2_Wound-healing_PC-3_cells.avi
A wound healing experiment with PC-3 cells, imaged every 5 minutes for 15 hours. Pixel size 1.24 µm.

To allow the user to check that CellTraxx runs as intended, all the results files after processing the above two videos are stored on Dropbox in the folder "Example_videos_for_testing_Results". 

To run CellTraxx on the first example video with the same settings as in the results files, copy the text from the file "1_celltraxx_defaults.txt" in the Dropbox folder "Example_videos_for_testing" to the file "celltraxx_defaults.txt" in the folder "C:\celltraxx_system\". Copy the first avi video file into the folder "C:\celltraxx_data\". Then run CellTraxx by double-clicking the celltraxx.exe icon or through ImageJ/Fiji as described in the user manual to utilize the interactive tuning option. 

To run the second example video, remove the first video from the "C:\celltraxx_data\" folder and paste in the second video. Copy the text from the file "2_celltraxx_defaults.txt" in the Dropbox folder "Example_videos_for_testing" to the file "celltraxx_defaults.txt" in "C:\celltraxx_system\", and run CellTraxx again.