Tuesday, 13 December 2016

Friday 9.12.16

Today's event:  Light-Field imaging;
Where and when: Friday 9th December 2016, 1pm-2pm, Andy's office (Room 246b, Physics and Astronomy, Kelvin Building, University of Glasgow);
Presenters: Laura and Guillem;
Presented: [1] Levoy, Marc, et al. "Light field Microscopy." ACM Transactions on Graphics (TOG) 25.3 (2006): 924-934[2] Cohen, Noy, et al. "Enhancing the performance of the light field microscope using wavefront coding." Optics express 22.20 (2014): 24817-24839[3] Georgiev, Todor, and Andrew Lumsdaine. "Superresolution with plenoptic camera 2.0." Adobe Systems Incorporated, Tech. Rep (2009); [4]  Broxton, Michael, et al. "Wave optics theory and 3-D deconvolution for the light field microscope." Optics express 21.21 (2013): 25418-25439.
Number of attendees: 22.

Second and last ICG Journal Club event of 2016, this time with many people from the Optics group too! 

Laura was the first presenter of the day, introducing the concept of light-field imaging discussing "Light field Microscopy", Levoy et al. 2006.
In a conventional image, each point contains information about the intensity of the light coming from one point of the imaged object. Instead, a light-field image contains, for each point of the imaged scene, information about the amount of light that reaches the imaging objective from different directions. This makes it possible to change the depth at which the image is focused or create perspective views of the imaged scene (all AFTER actually recording the image), and even reconstruct 3D volumes combining different refocused version of the same recorded image:
(image from "Light field Microscopy", Levoy et al. 2006)

In order to create these light-field images, an array of lenses is added to the imaging path of the microscope:
(image from "Light field Microscopy"Levoy et al. 2006)

Nothing comes for free though, and in light-field microscopy there is always a trade off between angular and lateral resolution. In the microscope presented in this article, each small lens in the lens array produces many images of the same point of the object, each corresponding to a different incoming light direction. In this case having more (and  smaller) lenses results in a better lateral resolution but a worse angular resolution.

This first paper raised questions about how the different final images are actually extracted from the recorded light-field image, and Laura also suggested an interesting article that discusses this topic in more details: 
Prevedel, Robert, et al. "Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy." Nature methods 11.7 (2014): 727-730. 

From there:
Light-field deconvolution.
The volume reconstruction itself can be formulated as a tomographic inverse problem27, wherein multiple different perspectives of a 3D volume are observed and linear reconstruction methods—implemented via deconvolution—are employed for computational 3D volume reconstruction. The image formation in light-field microscopes involves diffraction from both the objective and microlenses. PSFs for the deconvolution can be computed from scalar diffraction theory28.[...]"
[27] Kak, A.C. & Slaney, M. Principles of Computerized Tomographic Imaging (Society of Industrial and Applied Mathematics, 2001). [28] Gu, M. Advanced Optical Imaging Theory (Springer, 1999).
With Guillem and the three articles he presented we went into more details understanding how light-field imaging works, and we further discussed the deconvolution needed to reconstruct images focused at different scene depths.
Combining light-field imaging with wavefront coding, for example, it is possible to make the resolution of the reconstructed images vary/decade less when changing focusing depth:

We have only had two Journal Clubs so far, but it was enough for me to notice that I don't fully understand all the discussions that go on during these events, so I must admit I'm probably missing much of what has been said and discussed, but I hope this brief summary gives you an idea of what happened, and maybe even makes you want to come along next time too! 
Anyway, next time I'd better take some notes and also avoid waiting even just a few days before updating the blog!

We also had cakes and biscuits, as there always will be :)

Special thanks to: 
- The two presenters Guillem and Laura, for whom I hadn't prepared a star but who at least got one in the pictures;
- Pavi for smiling happily at my phone and not taking part in the Journal Club attendees new favorite sport of 'let's see who hydes best' :P;
- Miguel for helping me make sure there was no cake left at the end;
- Everybody for coming along!!

Thursday, 8 December 2016

Articles for tomorrow.

Sorry for not posting these titles before, I blame my poor organization this week to...Christmas coming soon, definitely. Let's see what excuse I'll come up with in January!
Anyway, better late than never, here are the articles that will be discussed tomorrow:

Levoy, Marc, et al. "Light field Microscopy." ACM Transactions on Graphics (TOG) 25.3 (2006): 924-934.

Cai, Zewei, et al. "Structured light field 3D imaging." Optics Express 24.18 (2016): 20324-20334.

Cohen, Noy, et al. "Enhancing the performance of the light field microscope using wavefront coding." Optics express 22.20 (2014): 24817-24839.

Pégard, Nicolas C., et al. "Compressive light-field microscopy for 3D neural activity recording." Optica 3.5 (2016): 517-524.

See you tomorrow at 1pm, and in the meantime have a nice Thursday!

Wednesday, 30 November 2016

Next event!

Next event: Light-Field imaging;
Where and when: Friday 9th December 2016, 1pm-2pm, Andy's office (Room 246b, Physics and Astronomy, Kelvin Building, University of Glasgow);
Presenters (confirmed for now): Laura and Guillem;
Coming soon: details on the articles that will be discussed.

After the JC, everybody back in the big office for a coffee, cakes and a free tour of our office Christmas decorations.

Sunday, 13 November 2016

Friday 11.11.16

Today's event: New approaches to optical design (a.k.a. weird optics);
Where and when: Friday 11th November 2016, 1pm-2pm, Andy's office (Room 246b, Physics and Astronomy, Kelvin Building, University of Glasgow);
Presenters: Ross, Stuart, Chiara;
Number of attendees: 11.

This first event of our journal club was dedicated to strange optical designs. We introduced the topic by discussing DARPA's program called "Extreme optics and imaging". The aim of this program is to develop, by 2020, some innovative optical components which should revolutionize the whole process of optical system design.

The way the problem is introduced is more or less the following:
At the moment we use optical components (like lenses) that follow certain simple physical laws (like the law of refraction) and with these we sometimes end up with very bulky and complicated optical systems (an example of this is the Mesolens we also talked about today). DARPA would like to break this paradigm and design new, specifically engineered, optical components. Light will interact with them in a much less straight forward way than what it does with lenses, gratings, filters and all the components we are now used to, but the idea is that they will simplify the design of multi-component optical systems.

Curiosity: as an example of what kind of thing DARPA has in mind, they always refer, in this presentation, to a sugar cube. At the beginning some of us thought 'sugar cube' was just chosen to give people the idea of a cubic object of more or less that size. Miguel then told me that a sugar cube can be thought of as a lens with very complex transmission matrix, so DARPA probably chose it to indicate not only a commonly known small cubic thing, but also an apparently simple object able to interact with light in a more intriguing way.

After I presented DARPA's program, Stuart introduced the Mesolens, an optical lens system specifically designed to allow 3D imaging of thick specimens  (6 mm wide and 3 mm thick) using confocal microscopy. The Mesolens gives low magnification, high depth resolution and big working distance, with the main drawback of being very big (image taken from [2]):

Ross concluded today's event with an article on flat lenses made of titanium dioxide nano pillars. Along the lines of DARPA's idea to overcome big unpractical optical systems, in this article the authors present a new type of lens, made of small titanium dioxide pillars instead of glass. These lenses can be manufactured to give a high NA, values of NA that normal lenses can achieve only being bulky (and expensive).

And for dessert...

That's all for now,

[1] DARPA's Power Point slides about the programprogram on DARPA's website.
[2] McConnell, Gail, Johanna Trägårdh, Rumelo Amor, John Dempster, Es Reid, and William Bradshaw Amos. "A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout." eLife 5 (2016): e18659.
[3] Khorasaninejad, Mohammadreza, Wei Ting Chen, Robert C. Devlin, Jaewon Oh, Alexander Y. Zhu, and Federico Capasso. "Planar Lenses at Visible Wavelengths." arXiv preprint arXiv:1605.02248 (2016).

Time to start a Journal Club!

New academic year, lots of new people just joined the group: perfect time to start a new Journal Club!...Or re-start? Has there ever been an Imaging Concepts Group journal club before?

Anyway, the idea to (re)start a group journal club had been around for a while, and in October Ross, Stuart and I (Chiara) decided to finally make it happen.

But no journal club comes without a blog! Or at least we say so, and so here I am, creating this blog, where I will keep records of what happens during our journal club events!

It's the first time I create a blog, so I'll probably spend the first weeks changing template and settings to see what I like the most. So far I've failed putting the picture I wanted as a background, and succeeded changing the text font and choosing colors for everything (2-1, come on, not too bad), plus, I'm confident I'll soon be able to upload pictures (very excited about that!).

About the ICG Journal Club:
We'll start by meeting once a month, on Friday at 1pm in Andy's office, and let's see how it goes! The first event took place last Friday (see next post) and next event will be at 1pm on Friday 9th of December, Andy's office (topic and papers to discuss still to be decided).

Ciao for now,
(mmmh..do people normally sign blog posts? well well, I think I like to :)  )