DeepDistance: A Multi-task Deep Regression Model for Cell Detection in Inverted Microscopy Images

TL;DR

DeepDistance is a multi-task deep regression model that improves cell detection accuracy in inverted microscopy images by learning shared features for multiple related tasks, including cell location and outer distance metrics.

Contribution

This paper introduces a novel multi-task deep regression framework with shared feature learning for cell detection, including an extended version with auxiliary classification, outperforming prior methods.

Findings

Successfully detects cells across different human cell lines.

Outperforms previous deep learning methods in cell detection accuracy.

Generalizes well to unseen cell lines.

Abstract

This paper presents a new deep regression model, which we call DeepDistance, for cell detection in images acquired with inverted microscopy. This model considers cell detection as a task of finding most probable locations that suggest cell centers in an image. It represents this main task with a regression task of learning an inner distance metric. However, different than the previously reported regression based methods, the DeepDistance model proposes to approach its learning as a multi-task regression problem where multiple tasks are learned by using shared feature representations. To this end, it defines a secondary metric, normalized outer distance, to represent a different aspect of the problem and proposes to define its learning as complementary to the main cell detection task. In order to learn these two complementary tasks more effectively, the DeepDistance model designs a fully convolutional network (FCN) with a shared encoder path and end-to-end trains this FCN to concurrently learn the tasks in parallel. DeepDistance uses the inner distances estimated by this FCN in a detection algorithm to locate individual cells in a given image. For further performance improvement on the main task, this paper also presents an extended version of the DeepDistance model. This extended model includes an auxiliary classification task and learns it in parallel to the two regression tasks by sharing feature representations with them. Our experiments on three different human cell lines reveal that the proposed multi-task learning models, the DeepDistance model and its extended version, successfully identify cell locations, even for the cell line that was not used in training, and improve the results of the previous deep learning methods.