Tracking

5-D Image Analysis

5-D Image analysis involves object extraction and tracking of multi-channel data. A typical dataset is shown on the right, with two types of T-cells that need to be tracked. It also has dendritic cells and blood vessels imaged in the same spatial context. The main framework for analyzing such a movie has been described in FARSIGHT_Framework. In a nut shell, we adopt a divide and conquer strategy in segmenting the different channels. We then track each channel individually and computer both intrinsic features, which are intrinsic to an object and associative features between an object and other channels.

(left)A sample 2-D projection of a single time snapshot from a 5-D movie from the immune system. (right)The corresponding tracking output

Tracking Program

Usage:

  track

Input parameters are contained in the file filename.conf located in the same directory of execution. It contains one row per 3-D image to be processed of the form

 DatasetID     "Filename"    channel_id     time_point

An example file look like the following lines

dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w1_t10.tif" 1 10
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w2_t10.tif" 2 10
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w3_t10.tif" 3 10
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w4_t10.tif" 4 10
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w1_t11.tif" 1 11
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w2_t11.tif" 2 11
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w3_t11.tif" 3 11
...
dataset1 "data/wF5p120307m1s5-t10/wF5p120307m1s5_w4_t14.tif" 4 14

First line represents one 3-D image of a movie named "dataset1" with filename "data/wF5p120307m1s5-t10/wF5p120307m1s5_w1_t10.tif". This file is from channel 1 and time point 10.

Output Files: The output files for the program are of 4 types.

• Unmixed files : Contains the individual channels after running our unmixing algorithm.
• Segmented files: Contains 16-bit images of the output of segmentation algorithm. Each cell in a time point has a unique index.
• Tracking output files: Contains 16-bit images of the output of tracking algorithm. Each cell in a time point has the index of its track.
• Feature files: Contains intrinsic and associative features computed after the tracking step.

Tracking Editor

Authors

The following people are involved in this project

• Arunachalam Narayanaswamy
• Ying Chen
• Ena Ladi
• Paul Herzmark