Bladder cancer (BCa) is the fourth most commonly diagnosed cancers in men and the eighth most common in women. It is an abnormal growth of tissues which develops in the bladder lining. Histological analysis of bladder tissue facilities diagnosis as well as it serves as an important tool for research. To bet- ter understand the molecular profile of bladder cancer and to detect predictive and prognostic features, microscopy methods, such as immunofluorescence (IF), are used to investigate the characteristics of bladder cancer tissue. For this project, a new method is proposed to segment cancer epithelial us- ing nuclei morphology captured with IF staining. The method is implemented using deep learning algorithms and performance achieved is compared with the literature. The dataset is stained for nuclei (DAPI) and a marker for cancer epithelial (panEPI) which was used to create the ground truth. Three popu- lar Convolutional Neural Network (CNN) namely U-Net, Residual U-Net and VGG16 were implemented to perform the segmentation task on the tissue mi- croarray dataset. In addition, a transfer learning approach was tested with the VGG16 network that was pre-trained with ImageNet dataset. Further, the performance from the three networks were compared using 3fold cross-validation. The dice accuracies achieved were 83.32% for U-Net, 88.05% for Residual U-Net and 82.73% for VGG16. These findings suggest that segmentation of cancerous tissue regions, using only the nuclear morphol- ogy, is feasible with high accuracy. Computer vision methods better utilizing nuclear morphology captured by the nuclear stain, are promising approaches to digitally augment the conventional IF marker panels, and therefore offer im- proved resolution of the molecular characteristics for research settings.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:kth-280383 |
| Date | January 2020 |
| Creators | Sharma, Osheen |
| Publisher | KTH, Skolan för kemi, bioteknologi och hälsa (CBH) |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | TRITA-CBH-GRU ; 2020:098 |
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