In recent years, the EU has observed a decrease in the stocks of certain fish species due to unrestricted fishing. To combat the problem, many fisheries are investigating how to automatically estimate the catch size and composition using sensors onboard the vessels. Yet, measuring the size of fish in marine imagery is a difficult task. The images generally suffer from complex conditions caused by cluttered fish, motion blur and dirty sensors. In this thesis, we propose a novel method for automatic measurement of fish size that can enable measuring both visible and occluded fish. We use a Mask R-CNN to segment the visible regions of the fish, and then fill in the shape of the occluded fish using a U-Net. We train the U-Net to perform shape completion in a semi-supervised manner, by simulating occlusions on an open-source fish dataset. Different to previous shape completion work, we teach the U-Net when to fill in the shape and not by including a small portion of fully visible fish in the input training data. Our results show that our proposed method succeeds to fill in the shape of the synthetically occluded fish as well as of some of the cluttered fish in real marine imagery. We achieve an mIoU score of 93.9 % on 1 000 synthetic test images and present qualitative results on real images captured onboard a fishing vessel. The qualitative results show that the U-Net can fill in the shapes of lightly occluded fish, but struggles when the tail fin is hidden and only parts of the fish body is visible. This task is difficult even for a human, and the performance could perhaps be increased by including the fish appearance in the shape completion task. The simulation-to-reality gap could perhaps also be reduced by finetuning the U-Net on some real occlusions, which could increase the performance on the heavy occlusions in the real marine imagery.