AY20/21 Special Term I Week 1 10-16 May
- Consultation with Tony in MnT lab
- Finalising project idea
AY20/21 Special Term I Week 2 17 -23 May
- Consultation with Dr Ho and Tony
- Designed block diagram
- Brainstormed on hardware needs for microscope control
AY20/21 Special Term I Week 3 24 -30 May
- Presentation with other groups
- Updated block diagram draft
- Designed 3D rough sketch
AY20/21 Special Term I Week 4 31 – 6 June
- MnT visit to try out microscopes in person with prepared yeast solution
- Prepared training data by taking 173 yeast cell images
- Dismantled remote controlled microscope project and got microscope
AY20/21 Special Term I Week 5 7 – 13 June
- Developed toy model for cell counting prediction
- Wrote preprocessing pipeline for model
- Prepared training data via manual labelling of cell images
- Flashed marlin onto a RAMPS board and demonstrated motion control
- Started writing code to do transfer learning over VGG and Unet model
- Wrote program to make labelling easier
- Worked on 3d printed design for webcam adapter and microscope tube mount
- Finished biological equipment ordering
- Attended 3D Printing workshop and Soldering and Circuits workshop
AY20/21 Special Term I Week 6 14 – 20 June
- Added data generator to toy model for custom data augmentation
- Prepared more training data via manual labelling of more cell images
- Assembled 3D Printed Frame
- Set up Raspberry Pi and Raspberry Pi Touchscreen Display
- Mounted RAMPS on aluminium profile of printer frame
- 3D Printing:
- Rail acceptor
- Lens Presser
- Camera supporter
- Camera holder
- Bottom Part of Microscope Stage Base
- Raspberry Pi Touchscreen Display Holder (Designing)
- Calibrated webcam
AY20/21 Special Term I Week 7 21 – 27 June
- Assembled base and fit back light into base
- Mounted webcam onto stage
- Reprinted microscope tube holder with correct dimensions
- Prepared and mounted sample with hemocytometer and pipette set-up and took pics from webcam
- Added fan to cool down Arduino
- Increased cell template types for synthetic dataset generation
- Generated 1.5k synthetic cell images, 300 each of 0,1,2,3,4 cells
- Trained toy model on 60/20/20 training/validation/test split
- Used alternate method contour detection for cell contour with image preprocessing with better performance
- Tried object segmentation using HSV pixel conversion and HSV range
- Used alternate method simple blob detector
AY20/21 Special Term I Week 8 28 – 4 July
- Draft and 3D print light blocker
- Draft and 3D print raspberry pi holder
- Draft and 3D print specimen fixer
- Improve stability of microscope mount by redoing holes and changing screw set-up
- Test out Flask interface written for axis control of microscope
- Test image loading within Flask Interface
- 3D print modified microscope stage base
- Tested out focusing algorithm with yeast slides
- Refined contour detection for webcam images and improved preprocessing
- Informal Progress Meeting with Dr Ho
AY20/21 Special Term I Week 9 5 – 11 July
- 3D Print new version of base prototype
- 3D Print new version of lens adaptor prototype
- 3D Print better quality light block bridge prototype
- Tested light blocker with webcam image capturing and show
- Tested cell counting model with raspberry pi
- Add new cell types and background to synthetic cell image generation so it imitates webcam images more closely
- Quantified cell counting model performance with synthetic dataset
- Change webcam config to video streaming mode to reduce lag between image captures
- 3D Print filament bulb stand prototype
- Presentation to Dr Ho, MnT staff and fellow peers
- Took clips for blog video editing
AY20/21 Special Term I Week 10 12 – 18 July
- 3D Print new version of filament bulb stand
- Tested focusing algorithm
- Improved focusing algorithm
- Prepared pondwater cell samples to try out different cells
- Filmed more clips for blog video editing
- Improved working autofocusing algorithm
- Improved synthetic dataset generation to handle more cells for the same image size
- Improved synthetic dataset generation to mock unfocused cells using blur filters
- Added sharpening function for image preprocessing
- Tried alternative thresholding algorithms for contour detection
- Static Thresholding with Edge Detection
AY20/21 Special Term I Week 11 19 – 25 July
- Finished editing blog video
- Worked on static thresholding cell-counting version
- Worked on alternate adaptive thresholding solution with modified preprocessing
- Tested out autofocusing algorithm
- Prepared algae cell samples in lab
- Tested out different thresholding solutions on images in lab
- Started working on the final presentation
AY20/21 Special Term I Week 12 26 – 1 August
- Final Presentation with Q&A and Individual Viva