Team:York/HP/Gold Integrated
Feedback on Software
Our initial holography software included no bandpass filter. However, after speaking to Dr. Kasprowicz (Phasefocus) about the quality of our processed images, he suggested that the variations in brightness would likely detract from the ability to use our software to render holograms that accurately represent the 3D space in a sample. He advised that we incorporate pseudo-flat field filtering into the software. We then spoke to Dr. Wilson (Department of Physics, University of York) about whether he had a method of implementing this. We came to the conclusion that incorporating the bandpass filter (that was already present in his own holography code) we could apply so-called proper-flat field filtering - which would achieve the same smoothening effect on the brightness of our processed images. We quickly set about adding this functionality to our software. Now, the version that we used to obtain all of the results presented here contains the option to use a bandpass filter. This is also available, released under GNU GPL, from our Downloads page.
We also had some helpful input from Dr. William Smith (Department of Computer Science, University of York) concerning cell counting with software. Originally, we intended to use the Hough transform method to find circles in our holograms' focal frames. Dr. Smith pointed out to us that, since we were also planning to look at non-circular organisms, we should apply blob-detection instead, since the Hough transform is only reliable for detecting near-perfect circles. We implemented this in the final version of the code we used to analyse our images. It is also available, under the same license and in the same place as above.
Feedback on Hardware
We decided that the design of our DIHM hardware should orient the optical axis in the vertical, despite initially testing the Raspberry Pi Camera Module on a horizontal bench. We did so because a horizontal design would lead to organisms moving, under gravity, towards one side of the analysis chamber. This presented a challenge in terms of developing an easily adjustable series of optical component holders. We intended to use an aluminium beam and drill holes in it at predetermined locations. Component platforms could then be attached in each location using nuts and bolts.
Andy White (Department of Electronic Engineering, University of York) suggested that, instead of this, we should use profile extrusion and fixings, making the height of each component platform much easier to adjust, with each adjustment requiring only that Allen screws be loosened, rather than completely removed. Additionally, there would be no limitation of positioning, since the platforms could be placed at any point on the extrusion, rather than only at predetermined locations. As can be seen on the Hardware page, we integrated this advice into our design.
