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kapoorlab authored Jul 2, 2024
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Expand Up @@ -15,30 +15,8 @@ TrackMate extension for oneat for verifying lineage trees

## Overview

Oneat is a keras based action classification library written by us and TrackMate-oneat is its Fiji extension that uses the results of detection of such cell events to correct lineage trees in TrackMate.
Oneat is a keras based action classification library written by us and TrackMate-oneat is its Fiji extension that uses the results of detection of such cell events to correct lineage trees in TrackMate. [More details](https://focalplane.biologists.com/2022/07/04/trackmate-oneat-auto-track-correction-using-deep-learning-networks/)

# Tracking Metrics
## Computational Support

Linking max distance: 14 micron, Gap closing max distance: 16 micron, Gap closing max fra me gap: 3, splitting max distance: 15
Initial tracks: 570

### Simple LAP tracker

{DET : 0.9968, CT : 0.7221, TRA : 0.9945, TF : 0.9808, BCi : 0}

### Simple LAP tracker + Oneat

{DET : 0.9968, CT : 0.7247, TRA : 0.9945, TF : 0.9771, BCi : 0.3404}

### LAP Tracker with track splitting

{DET : 0.9968, CT : 0.454, TRA : 0.9908; TF : 0.8830, BCi : 0.063}

### LAP Tracker with track splitting + Oneat

{DET : 0.9968, CT : 0.456, TRA : 0.9636, TF : 0.8713, BCi : 0.2857}

## Videos

In this video I compare the tracking results using LAP tracker of TrackMate and SimpleLap tracker + oneat correction.
[LAP tracker comparision with SimpleLAP Tracker + oneat correction](https://youtu.be/9HZvWxr2fsY)
Auto Track Correction using TrackMate-Oneat was granted access to the HPC resources of IDRIS under the allocation 2022 - [AD011013724], 2023 - [AD011013724R1] made by GENCI. We used the resources to create training data and inference on the imaging datasets.

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