Wrap-up of FiO/LS 09

The last day was fun. Well, not because I was waiting for the conference to end; but because apart from interesting talks, I had great time meeting Jim Fienup’s group over lunch and guys from different labs before we left San Jose.

I had good fun attending Wonshik Choi’s and Laura’s talks about phase-retrieval. Wonshik’s invited talk (FThB3) was about diffraction tomography (where you indeed measure phase information along many angles in contrast to intensity diffraction tomography I mentioned in previous post). What impressed me was that he understood and explained all assumptions involved in acquisition and reconstruction in simple terms. Laura extended transport of intensity equation (TIE) in two interesting directions. TIE relates axial derivative of intensity of  a beam to transverse distribution of phase as it propagates. By measuring intensity at two slightly defocused planes, one can retrieve specimen phase using TIE. One of her talk (CThA3) showed how one can include  higher-order derivatives of the axial intensity in this formulation. In the other (rather cool) talk (FThR3), she showed how one can use off-the-shelf color camera and exploit chromatic axial shifts  introduced by imaging system to record intensities at two slightly defocused planes. This makes it possible to perform TIE with single snapshot.

Over lunch, I met  Jim Fienup and his group and learned some new things about phase-retrieval and Rochester. Just before we left the conference venue, Laura & Lei (MIT), Naveen & I (Singapore) and Mayukh (Rochester) sat down to chat about peculiarities of our countries and (ahem!) our advisers. Mayukh, who works with Prof. Emil Wolf recounted many interesting stories that Emil has recounted to him. We had stories heard from Colin to share. So the day ended with healthy dose of laugh.

This ends my first trip to the US and I had a great 12-day stay here. I have written this and the previous posts from the airport and I think everyone else is traveling too. Who wants to stay back in San Jose:)? So bon voyage.

Wednesday at FiO – More computational imaging, phase-space anlaysis, and phase-retrieval

I know this post is late, but I hope it is worth the wait (if anyone was waiting ). My energy levels were just not sufficient for me to write anything coherent at the end of the fourth day of conference, but I am feeling better now that the conference has ended. So let’s begin with events of Wednesday.

Wednesday’s program convinced me that parallel universes do exist. I was shuttling between ground floor and first floor (aka banquet floor) trying to pop-in and pop-out of talks at right times. Keeping with theme of last post, I will point out one talk each from above three areas. As a bonus, I also point out how my talk went.

Computational imaging:

The first session of the day that I went to was the joint interdisciplinary session of AO/COSI/SRS. The talk that I remember clearly is Marc Levoy’s on light-field photography and microscopy (JWA3). Marc has visited Singapore earlier and given a similar talk. So he had advised me against attending his talk and spend time gathering something new. But it was good to see how he is planning to apply these methods to decoding of neuronal wiring in zebra fish (or another?) embryos. The idea is to stimulate neurons located at arbitrary 3D locations using light-field illumination architecture. This ’stimulate firing’ of neuron should be followed by fast 3D imaging of activation of neighboring neurons. Yes, the neurons have to be labelled correctly – you need to label neuronal ion channels (rhodopsin) in such a way that when the label is excited the channel opens. Plus, all neurons have to be labelled with calcium indicator dye which indicates when certain neuron becomes active. The enabling technology in labeling is genetic modification of the zebra fish to express these proteins in live animals.

Phase retrieval:

The next noteworthy talk I attended was Greg Gbur’s (SWA1) on intensity diffraction tomography. The idea is rather neat – you measure the phase of the specimen by tomography but without explicitly measuring phase (e.g. by interferometry or otherwise). The idea relies on the fact that phase information of the specimen does affect intensity of diffracted light and hence one ought to be able to retrieve the phase distribution from intensity measurements alone. I should note that similar goal is achieved in a different way by transport of intensity formulation.

In the same session was my talk about registration of gradient information (SWA4). We know that traditional methods of image registration are meant to register measurements of the same function. Therefore, when we want to register gradients of some function along X and Y directions, these methods don’t work. I figured that registration of gradients requires that you reformulate the registration problem and devise a new procedure for computing the registration information. This registration has allowed me to accurately reconstruct phase information from phase-gradients that I measure with differential interference contrast (DIC) and differential phase contrast (DPC). I did better at this talk than the one on Monday and had some useful discussion after it. I was helped by the fact that the speaker after me had withdrawn, giving me more time to delve onto details.

Phase-space analysis:

It was pointed out by Prof. William Rhodes that Wigner distribution computed from discrete samples of a signal may contain erroneous structures (FWW1). This happens because when a temporal signal is sampled, it becomes periodic in frequency with the period equal to the sampling frequency. These periodic components of frequency produce cross-terms. These cross-terms cancel out if one projects the signal along frequency (to obtain signal intensity) but do not if one projects the signal along space (to obtain spectrum density). These errors are exacerbated when one operates on this distribution (e.g. propogate by shearing) and then again tries to compute intensity or spectral density by projection.

The day 2 – fascinating plenaries, informative sessions and student reception

The second day at FiO turned busy and occupying. So busy that at the end of the day, I had to crash in the bed. This blog is therefore coming little late.

Bob has provided great near-live update of the plenary talks. The plenaries were really fascinating and enthusiasm of plenary speakers really palpable. Prof. Andrea Ghez made one of the best presentation I have ever seen and I hope to emulate her in future. The slides didn’t have more than 5 lines of text and a single graphic, which kept audience focused on what she was saying. I learned for the first time that there is likely a black hole at the center of every galaxy and its region of influence is called Schwarzchild radius. It is the radius below which a given amount of mass will collapse under the influence of gravity. It was fascinating to learn that the earth’s Schwarzchild radius is of the order of sugar cube and of the sun is of the order of a small university campus. However, I didn’t follow the notion that some galaxies have active nuclei that emit enormous jets of gas from their centers. If there is a black-hole at the center, how does that gas escape? Perhaps this gas escapes while whirling around the black hole at the edge of the Schwarzchild region. These ideas were followed by a discussion about the development of adaptive optics and impressive improvements that it provides when imaging stars.

Dr. Janos Kirz started from the origins of X-ray microscopy and brought the audience up to date with the state of the art. In effect, he summarized the key developments of the whole field in half an hour! It was curious to know that the refractive index of  some materials at  X-ray wavelengths is less than 1 and hence one can have total external reflection – a situation that I think does not exist (yet) in optical regime. He described idea of lens-less imaging in very intuitive terms. Basically, a lens can be thought of as returning us an object from the diffraction pattern. But if one records a diffraction pattern, the object can be retrieved by computation – bypassing practical issues of making a lens in X-ray regime.

Afterward, I attended sessions related to biomedical optics at Glen Ellen and gave a talk (about phase-space models for partially coherent systems) in the later half of the afternoon. All talks were interesting and some were really informative. It was great to see how non-linear optical method of CARS is giving molecular information without the need of labels. Several presentations were about design, implementation and application of new microscopic contrast mechanisms. I felt my presentation was well received and I could convey the big picture. But perhaps I put forward too many details. I felt so because some in the audience asked me to send more information rather than asking questions themselves. I hope to do better  at my next talk on Wednesday.

The day ended with a relaxing time at O’ Flaherty’s pub – the venue  of OSA student member reception. It was great meeting friends from all over the world and sharing their experiences. As I said earlier, I had to crash in the bed at the end.

Frontiers in Optics (FiO)

Hello world,

I am excited at the prospect of attending this year’s Frontiers in Optics (FiO) for the first time. I am looking forward to its collegial flavor and high-quality work  in areas of basic optics, information processing, and microscopy. I also happen to be one of the official bloggers for FiO. I am not sure if this is the first year of inviting prospective attendees to blog about the conference, but it is a great idea for receiving honest feedback about the event. The message to the official bloggers from the OSA was not to be ’sales-persons’ for the conference but reporters true to their observations. Did I mention FiO is collegial? I look forward to meeting in person people coordinating this blogging effort – KiKi, Janessa, and Robert.

I haven’t yet sorted out finances, but I am hopeful. I am going to present two papers at the conference:

• The first one is about modeling of imaging  methods that use large illumination apertures (termed partially coherent imaging methods). A brief abstract can be found here. This work generalizes our approach of modeling the  differential interference contrast (as published in Optics Express here).
• The second one has more of an image processing flavor. It is about registration of gradients of given function. Registration of multiple measurements of a  2D function is well-studied in the form of image registration based on intensity correlation. But this framework is not applicable to registration of images obtained with microscopic methods that measure gradients of specimen’s optical thickness. I extend a robust image registration method of phase correlation to registration of gradient data. Abstract is here.

Our group has recently caught interest in phase-space representations (whose patent identity is Wigner distribution function) of optical signals and systems. I am particularly interested in phase-space analysis and design of partially coherent imaging systems. A useful review about phase-space optics can be found on Dr. Martin Baastian’s site who is one of the leaders in this area. It is great that FiO is going to have a special symposium on these ideas. Information about this and other special symposia is here. If you are going to be at the conference and have similar interests, we should meet up!

When it comes to optics conferences, a few come to mind just because of their shear size: OSA’s Frontiers in Optics et al., OSA’s Conference on Lasers and Electro Optics et al., SPIE’s Photonics West (PW), and SPIE’s Photonics Europe.  The ‘et al.’ hints to the fact that all of these are actually ’super-conferences’ comprising of multiple conferences. SPIE tends to consider each technical session a conference and therefore there are tens of simultaneous conferences. OSA on the other hand likes an approach of bringing together a set of large conferences. These large conferences let you find connections to your work in other fields. But you may feel lost among lots of parallel sessions and too many ideas ringing in your head.

Spatial light modulators (SLM)

Recently, I have got interested in spatial light modulators (SLMs). SLMs are to optics what programmable logic is to computing. They allow modulation of certain properties of light (e.g., amplitude, phase, polarization).  I thought of noting down my finds about available technologies and update them as I stumble upon new information. A good question to ask is – ‘what do we precisely mean  by modulation’? Modulation here means changing two dimensional distribution of amplitude, phase or polarization of light at given plane. I am particularly interested in amplitude modulators for automating our new quantitative imaging method based on oblique-illuminaiton.  Here are links to our conference abstracts and a journal paper:

• “Quantitative phase-gradient imaging at high resolution with asymmetric illumination-based differential phase contrast” in Optics Letters 2009
• “Linear Phase-Gradient Imaging with Asymmetric Illumination Based Differential Phase Contrast (AIDPC)” @ Novel Techniques in Microscopy 2009
• “Full-field phase-gradient contrast methods for label-free quantitative imaging of cellular morphology: AIDPC and DIC” @ Focus on Microscopy 2009
• “Asymmetric illumination based differential phase contrast (AI-DPC) for full-field transmission imaging of phase information in biological specimens” @ Focus on Microscopy 2008

I classify the spatial light modulators depending on the type of modulation they are designed to provide. Most of the time, one would like to modulate either amplitude, phase, or polarization without affecting the other properties. In basic optics research, SLMs are widely used for phase modulation in areas of holography, optical communication, optical trapping, beam shaping, adaptive optics etc. In commercial applications, amplitude modulation dominates where SLMs are used for writing dynamic patterns that are projected. Polarization modulation has been used in design of programmable spectral filters called Lyot filter and quantitative birefringence imaging devices called Polscope. As noted next,  all SLM technologies except for digital micro-mirror devices (DMD) and deformable mirrors employ birefringence modulation under electronic control for achieving amplitude, phase or polarization modulation. Most of the birefringent reflective devices seem to use LCoS (liquid crystal on silicon) technology. Reflection based geometry allows putting control logic behind the liquid crystals leading to high density and possibility of calibration. In transmission SLMs, the logic is implemented around the pixels which limits amount of intelligence (e.g. calibration circuit) that can be built in and causes spurious diffraction.

Amplitude modulators:

If you want to perform binary modulation (black and white), digital micro-mirror devices (DMD) and ferroelectric liquid crystals (FLC) are the technologies of the day. For grayscale amplitude modulation, twisted nematic liquid crystal (TNLC) devices seem to be the most suitable.

• DMDs are micro-mechanical devices in which a tiny mirror is mounted on a semiconductor chip whose orientation is controlled by currents produced on the chip under programmable control. Texas Instruments invented DMDs for projection applications with goal of substituting the roll of film by this single device. DMDs are fast and one can update the patterns at the rate of MHz. Advantages of DMDs include nearly-polarization-insensitive modulation, fast switching time, high damage threshold, and low cost. But, they are bit awkward to use because of their reflection based geometry which requires oblique illumination to separate unmodulated and modulated light. There are some prism-based optical modules noted on TI website which provide easy integration of DMD in light path.
• FLC devices use bistable liquid crystal whose birefringence can be switched at MHz rate. By placing FLC between two crossed or parallel polarizers, one can perform binary  modulation. They are little pricier than DMDs and available from Displaytech. Depending on your application, FLCs polarization sensitive operation may be an advantage or disadvantage. They operate at lower power than DMDs and allow smaller pixel sizes. They can be used in reflection (which is frequent) or transmission.
• Both types of black and white technologies can mimic grayscale modulation due to their fast switching speed. Grayscale modulation can be achieved by temporal modulation  at rates much faster than integration time of the detector. This works fairly well with commecial projection applications as visual integration time is around 33ms (1/30 s).
• True grayscale modulation can be obtained with twisted-nematic liquid crystal (TNLC) devices, which again can be used in transmission or in reflection between polarizers.  Holoeye and Meadowlark both supply twisted-nematic LCDs. Holoeye is very active in design and support of TNLC SLMs. Their reflection-type device LC-R 1080 is based on liquid crystal on silicon (LCoS) technology and designed for amplitude modulation. Most of the commercial displays are based on TNLCs, so you might source one from an unused display projector. Holoeye  provides an OEM kit (HEO 0017) based on a commercial display from Sony and costs nearly half in comparison to its reflection devices.

Phase modulators

• (Thanks to Laura, friend at MIT, for reminding me about deformable mirrors) The most extensively used devices for phase-modulation are deformable mirros (DM).  There are several technologies for realizing DMs.  Conceptually, DM can be thought of as a flat stretched reflective membrane mounted on actuators. The actuators deform the membrane as per required phase modulation. They are widely used in astronomy, retinal imaging, microscopy research, and pulse shaping. Several companies provide DM and phase-modulation kits suitable for above application, a noteworthy among them being Boston Micromachines.
• With TNLCs, one can control the phase distribution of light but perhaps accompanied by spurious amplitude modulation. However, Holoeye combines twisted nematic LCs with intelligent voltage control to negate spurious amplitude modulation with its pluto and HEO 1080P devices.
• A competing technology is  Parallel aligned liquid crystal (PALC). PALCs twist along the propagation axis rather than around it. They do not rotate polarization of input light but merely change refractive index seen by it. Hence, they allow pure phase modulation. Such devices are available from Hamamatsu.

Polarization modulators

• These modulators are usually used for variable retardation, i.e. to control ellipticity of light. TNLCs are again widely used for this purpose. In fact, the basic mechanism of TNLC modulation is to alter the 2D distribution of polarization of light, which is then converted to amplitude or phase modulation with help of polarizer on the output side. Arcoptix and Meadowlark supply devices meant for programmable retardation, generation of radially or azimuthally polarized light, etc.

Be careful when you use scan zoom on confocal

Hello World,

After some beautiful pictures on this blog here is a little gory one. I was trying to take some images of certain type of nuclei in my cell sample. The procedure I followed was – take an image at minimum scan zoom, identify the region of interest (ROI), select that ROI and let the laser scan only that region – effectively zooming in to the ROI. Every time I would select an ROI and apply the scan zoom, I would see mysterious looking distortions – as if there was a water bubble on top of the region being scanned. I was using a water immersion lens at that time, so thought something was really wrong in the way I was putting water drop on the coverslip. Even after repeated attempts at draining and wetting the coverslip, I couldn’t get rid of distortion. Then it occurred to me that I should take an image at lower zoom after I produce such distortion.

That image revealed that I was frying the cells at high scan zoom – I was putting too much laser power in very small physical area!! See a circular ‘burn mark’ in following image. Also notice how the burn mark causes warping of signal coming from fluorescent probes. Effectively, burn mark acts as a lens. I am still not sure if the cells were ablated by local heating or the mounting medium evaporated.

When we scan the laser over area zoomed, by say, factor of 50 – the average laser intensity in the scanned area also goes up by 50. And it proved too much for cells to handle. So it is good idea to reduce the laser power when you use the scan zoom in your imaging experiments as you focus on smaller and smaller areas.

But I wonder why local heating was prominent only in the circular path and not throughout the scanned area.

Can anyone throw some light?