Cell Culture Assistive Application for Precipitation Image Diagnosis

TL;DR

This paper presents an automated machine learning application that detects and visualizes precipitation artefacts in images of 384-well plates, improving consistency and efficiency in regenerative medicine research.

Contribution

It introduces a novel pipeline combining contrastive clustering and anomaly detection to accurately identify small precipitation features without image resizing.

Findings

Effective precipitation detection in high-resolution images

Visualization of precipitation distribution on well plates

Improved consistency over manual inspection

Abstract

In regenerative medicine research, we experimentally design the composition of chemical medium. We add different components to 384-well plates and culture the biological cells. We monitor the condition of the cells and take time-lapse bioimages for morphological assay. In particular, precipitation can appear as artefacts in the image and contaminate the noise in the imaging assay. Inspecting precipitates is a tedious task for the observer, and differences in experience can lead to variations in judgement from person to person. The machine learning approach will remove the burden of human inspection and provide consistent inspection. In addition, precipitation features are as small as 10-20 {\mu}m. A 1200 pixel square well image resized under a resolution of 2.82 {\mu}m/pixel will result in a reduction in precipitation features. Dividing the well images into 240-pixel squares and learning without resizing preserves the resolution of the original image. In this study, we developed an application to automatically detect precipitation on 384-well plates utilising optical microscope images. We apply MN-pair contrastive clustering to extract precipitation classes from approximately 20,000 patch images. To detect precipitation features, we compare deeper FCDDs detectors with optional backbones and build a machine learning pipeline to detect precipitation from the maximum score of quadruplet well images using isolation Forest algorithm, where the anomaly score is ranged from zero to one. Furthermore, using this application we can visualise precipitation situ heatmap on a 384-well plate.