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Considerations and Justifications for Choice When training the deep learning model (see Deep Learning (Multiclass Classification with CNN) for more information),  generating a synthetic dataset was helpful for increasing the size of the training and validation dataset to improve model performance. Subsequently, even after moving away from deep learning models — which meant a negation […]

Motivation Cell counting is contingent on having a focused image. Since our objective lens configuration has a fixed focal length, we can vary its height to bring the image to focus. However, the working range in which the image is focused is rather small. In this blog, we will discuss how we quantify the extent […]

Considerations and Justifications for Choice We decided to experiment with different methods to explore alternatives not commonly mentioned in literature related to automated cell counting. As we are using yeast cells for our samples, their simple, near-circular cell shape would be suitable for blob detection as they can be identified according to their enclosed areas. […]

Considerations and Justifications for Choice After conducting preliminary research on common cell-counting models [1][2], we settled on experimenting with deep learning first. We decided to utilise a classification approach. By cropping the microscope images into multiple pieces, the range of cells in each piece would fall between 0 and 5 cells. The model would then […]

Principles Template-matching uses pre-defined images (hence ‘templates’) to execute a search in a separate image. It involves convolving the template image over the target image, and in effect can be understood as a form of cross-correlation: both images are signals in space, and if they are strongly correlated at a few specific points, we can […]

Motivation We sought out to control the mechanical degrees of freedom for the microscope. On a practical level, the microscope should have (1) adjustable focus, (2) have the ability to sweep over a larger sample.  Adjustable focus The microscope uses a fixed objective lens, with a fixed working range and fixed focal length. A biological […]

Considerations and Justifications for Choice We are in the process of trying out alternate light sources to see if there is any improvements for the webcam images and lighting of the cell sample. Currently, our set-up uses a LED light. We decided to try a filament bulb. A support structure is needed to prop the […]

Week 1 10-16 May We kicked off with an initial consultation with Tony in the Making and Tinkering lab. After pitching our idea of a 3D-printed microscope with automated cell counting, we obtained feedback on the feasibility of the project and guidance on how to implement what we want to do. We will have to […]

Problems Encountered in 3D Printing We learnt how to use Autodesk Fusion 360 from scratch. Remote collaboration on Autodesk Fusion 360 was a chore as there were lags in the system. It was better to design and edit with group members face to face.  The printed model from our drawing on Autodesk Fusion 360 may not […]

Considerations and Justifications for Choice We decided to adopt the stage clips from the original microscope to secure the sample slide in place on the microscope stage. The stage clips have horizontal screw holes and cannot be screwed directly onto the microscope stage. Hence, a secondary piece (specimen fixer) is required to accommodate the screw […]