Deep Learning-Based Image Analysis for Microwell Assay

Sammanfattning

This thesis investigates the performance of deep learning models, specifically Resnet50 and TransUnet, in semantic image segmentation on microwell images containing tumor and natural killer (NK) cells. The main goal is to examine the effect of only using bright-field data (1-channel) as input instead of both fluorescent and brightfield data (4-channel); this is interesting since fluorescent imaging can cause damage to the cells being analyzed. The network performance is measured by Intersection over Union (IoU), the networks were trained and using manually annotated data from Onfelt Lab. TransUnet consistently outperformed the Resnet50 for both the 4-channel and 1-channel data. Moreover, the 4-channel input generally resulted in a better IoU compared to using only the bright-field channel. Furthermore, a significant decline in performance is observed when the networks are tested on the control data. For the control data, the overall IoU for the best performing 4-channel model dropped from 86.2\% to 73.9\%. The best performing 1-channel model dropped from 83.8\% to 70.8\% overall IoU.