Large field of view microscopes for mouse brain imaging

For typical confocal or two-photon microscopes that maintain (sub)cellular resolution, a high-magnification objective is needed (typically 16x, 20x or 25x). This in turn limits the field of view (FOV) to ⌀ 1.0-1.5 mm.

For imaging in the mouse brain cortex, which is basically a big unwrinkled surface of a size of the order of 10 mm, a bigger FOV would be nice to have for some applications. Recently, a couple of papers came out that tried to increase the FOV, while using optical engineering to maintain the resolution. (Please don’t hesitate to tell me if I missed a relevant publication.)

Few years ago, I would have expected such papers to be published in Nature Methods, but apparently the time has come where optical engineering and improvement of existing techniques is not considered enough for passing the novelty bar. However, the three papers offer some very interesting lessons on engineering a two-photon microscope, of which I want to pick a few:

  • The use of large-aperture (15 mm) galvo scanners by Tsai et al. in order to avoid large scanning angles that would create large aberrations. (Thus the design cannot be used with resonant scanners which have much smaller apertures.) The large beam diameter at the galvos allows to use a low-magnification scan lens-tube lens pair, which demagnifies the scan angle to a lesser extent. It is important to understand that the scan lens-tube lens telescope magnifies the beam diameter, but at the same time decreases the scan angle by the same factor.
  • Due to the extremely large and heavy costum-designed objectives (click here for a picture of the Stirman et al. objective [update 2018: the picture has since been removed]), remote focusing is necessary for fast switching of the axial focus. Stirman et al. use optotune lenses; Sofroniew, Flickinger et al. take advantage of a remote mirror technique that has been developed 2007-2012, but use a voice coil motor for mirror displacement – interestingly, I had converged onto the same solution when I constructed my z-scanning module (see this previous blog post or the dedicated paper).
    The optotune solution by Stirman et al. is in my opinion less well-suited for remote scanning, since resolution cannot be maintained over large z-ranges due to optical issues (although this is not mentioned in the paper). It’s probably good enough for small z-ranges, but it has to be considered in the optical design from the beginning.
  • Sofroniew, Flickinger et al. use something they call a virtually conjugated galvo pair (VCGP) to avoid annoying relay optics. I do not understand why they came up with this strange name or whether this design has been used before, but the principle is quite nice.
  • Stirman et al. use temporal multiplexing to image two independently chosen locations using separated, delayed light paths, similar to this 2011 paper (also check out this thesis for less polished pictures).
  • A chapter that I found interesting to read is “Tolerancing and sensitivity analysis” in the Stirman et al. paper.
  • Sofroniew, Flickinger et al. employed oil interfaces close to the PMT surface to increase the photon collection NA.
    On a related note, it is interesting to read their speculations about inhomogeneities of the PMT photocathode.

The problem with these microscope designs is – how to adapt them to one’s own lab? The goal should be to generate something which does not work for a paper only, but as a reliable and robust tool. I can see two (non mutually exclusive) possibilities how this could be achieved. The first is transparency, with the free and open distribution of Zemax files and software to anybody who wants it. In this spirit, I liked a lot figure 2 in the paper by Sofroniew, Flickinger et al., because it clearly shows the optical design a) as a scheme, b) as a CAD drawing, and c) as a real life picture.

A second way would be to license the design to companies like Scientifica, Thorlabs or maybe even smaller spin-offs/start-ups like Neurolabware or Vidrio Technologies. Similar to turn-key femtosecond lasers that revolutionized the field of 2P microscopy when they became available, one can hope for a company that puts together modular units that are stable, robust and working out of the box to enable complex microscopes (with z-scanning, with multi-region scanning, with simultaneous spatially patterned optogenetics, with multiple detection channels, with >1100 nm coatings for excitation, with adaptive optics for deep tissue imaging, etc.) in normal neuroscience labs. I’m probably not the only one who is fascinated by these technologies, but if someone has a neuroscientific question, he does not want to spend his whole life on the development of a high-end microscope. (Moreover, it would not be very rewarding, because this type of engineering and optimization process will not be rewarded by any kind of top-level publication.) Similarly, nobody wants to build his own femtosecond-pulsed laser for 2P imaging these days (although there are always exceptions, for example this one).

This entry was posted in Calcium Imaging, Imaging, Microscopy and tagged , , . Bookmark the permalink.

7 Responses to Large field of view microscopes for mouse brain imaging

  1. There’s a nice review in Nature Neuroscience by Ji et al. that covers wide FOV 2P microscopes, as well as other relevant technical details for 2P scanning microscopes:
    It is the review I always missed, simply gathering all the relevant references. If anything, I miss a more detailed discussion on how to improve collection optics, but there are also not many publications out, few of which can be easily adapted to an existing setup.

  2. Joshua Trachtenberg says:

    If you’re at SFN in San Diego, swing by our booth (Neurolabware) and talk with Adrian. We should have our own wide FOV on display. Dario will likely be there for only a day or so.

  3. Jeffrey Stirman says:

    Jeff Stirman here. In the spirit of adapting these custom systems to one’s lab, we opted for transparency and gave all optical prescriptions in the Supp Material of our paper. Someone can always use this as a starting point if you wanted to design your own. Sofroniew et al went a different direction and Thorlabs is now selling their scope. There are of course advantages and disadvantages to both.

    The virtually conjugated galvo pair (VCGP) employed by Sofroniew is a great solution (it can only be done in one direction), but can lead to aberrations (as they mentioned briefly) one must carefully consider. Other methods of optical relay have been investigated (off-axis parabolic mirrors, spherical mirrors w off axis asperical element (see David Kessler patents)). These are particularly attractive as they are largely achromatic. Note that all large FOV scopes (and many commercial systems) are using some type of X to Y relay. It has been shown previously that close-coupled systems can lead to significant aberrations, and in general probably avoided.

    As for the focusing, we chose to use the liquid lens for simplicity. It is correct that it can add aberrations to the system as change in focus is applied. This can be minimized and, as we showed, lead to little changes in PSF. Our moderate NA also decreased the influence of the liquid lens. The influence of most remote focusing systems can easily be assessed in optical design programs (Zemax) and should be done. I do like the use of voice coils for movement as both you and Sofroniew demonstrated: this is an elegant solution.

    Thanks and great blog!

    • Hi Jeff,

      Thanks for your comment, and many thanks for sharing the optical prescriptions in your paper, which I really appreciate. – By the way, I do not really see why an ultra-wide field-of-view microscope sold by Thorlabs should not make open all optical prescriptions as well. First, if someone wants to change some minor optics, replace a broken part or couple in another light-path, it is certainly helpful to have open access to the optical design, without the need to ask the company anything. (On a similar note, I also disliked that the most recent versions of Scanimage do not make all of the Matlab code openly accessible.) Second, it is unlikely that another company will come, build the same microscope and try to outcompete Thorlabs – the market is simply not big enough, I would guess, and the microscope too expensive.

      Thanks for your comments on relay optics and the liquid lens. I wanted to try out ETLs to see how they work in practice, but I have not yet found the time to do so.

  4. Femtonics says:

    At SFN2018 in San Diego you can take our mesoscope objective in your hand.
    Stop by our booth #535.

    • Hi, I will not be at SfN in 2018, but it’s good to know that you are working on this kind of objectives as well. I’d be interested in the resolution that you are getting across the FOV!
      Best, Peter

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.