Posts archived in Hardware
Thorlabs and Newport have offered 3D models of their products for a long time. However, they’re typically in formats for expensive programs like SolidWorks and AutoCAD. In the past year or two, Newport has been slowly adding to their library of Google SketchUp models.
I still prefer SolidWorks, but I’m optimistic that I’ll eventually switch to SketchUp. Regardless, it’s nice to see a company supporting free tools.
December 30, 2011
Optics Planet has a nice selection of inexpensive microscopes and other lab equipment. Such as these chubby, potential Cute Overload stars from Nikon (above, the blue one that is taking a bow is $380).
Braintree Scientific also has a really nice selection of reasonably priced equipment. Tons of very interesting, unique products. Get the catalog and flip through it– the website isn’t so nice to browse. They do custom work too, in case you have something specific in mind. One of their new products is a netbook+syringe pump package, pictured below:
I recognize the syringe pump as one of New Era’s OEM pumps. New Era sells all kinds of syringe pumps, from barebones OEM devices ($500, controlled via RS-232), to digital ($750) and multi-syringe units ($1500). You can use one of the OEM units for things like delivering water rewards in behavior rigs.
Thorlabs’ scope pieces and kits have been mentioned in these pages before. At SfN, they had their new B-scope on display. This is like the Sutter MOM and the UCLA scope, in that the microscope rotates in one plane in addition to x-y-z movement. A few differences with the Thorlabs scope:
1. The objective rotates around the focal plane, and the rotation is motorized.
With the Sutter/UCLA style scopes, the objective rotates about an axis along the scan path, so the focus point changes a ton when rotating. The rotation can really only be changed before there is a prep on there, because the objective swings a big arc whenever the rotation changes and it ends up pointing at a completely different point in space.
By contrast, the Thorlabs scope is set up to rotate about an axis that is in the plane of focus. So you can be looking at a cell and then, while imaging, rotate the scope (since it’s motorized) and still keep looking at the same thing, just from a different angle.
This is why they have the crazy periscope you can see to the right in the photo below.
I remember seeing a scope with this same feature (rotation around an axis in the image plane) at a conference at least 2 years ago. I think it was a group based out of Switzerland. Can anyone fill in the details for me?
2. No conventional scanners, just the Thorlabs conventional scanners.
This might not be true for long. Thorlabs has their own conventional scanners, but they’re not as fast as Cambridge Technologies (CTI) scanners. This is probably why they opted to put their resonant scanners in the system.
I’m guessing that they’ll help out buyers if they want to fit the scope with a set of conventional scanners from CTI. I say this because Thorlabs told more than one person at SfN that they would help them fit the Thorlabs resonant scanner kit to their Sutter MOM scope. This was news to Sutter.
The original post on building a 2p scope still gets a lot of hits. Let’s revisit the topic.
Scientifica has been working hard on developing a kit for multiphoton imaging. It’s all based off of their minimalist, yet versatile SliceScope platform.
I’ve had the opportunity to check out their collection module and it’s really well done. The components are available for individual purchase, so if you just want to buy part of it and tack it onto something else you’ve got, they offer that flexibility. Since they sell a wide range of electrophysiology products, they can offer customized package deals to suit your needs.
The collection module shown above is a nice tight package with the PMTs, filter cube, and preamps all integrated. They really like the R9880U series. I can see why: they’re very small, with an 8 mm diameter active area, and are constructed such that incident light can approach from a wide angle. However, they are bialkali and the QE at 520nm is less than 30%. They have a GaAsP version in the works.
Their platform can be configured for slices (below, left) or in vivo (below, right).
Thorlabs has made some improvements in their own software for their 2p kit, and Vijay Iyer’s ScanImage 4 will interface with the resonant scanners. I think this is an interesting starting place for custom rigs. Thorlabs has add-ons like deformable mirrors that you can purchase at a later time. There’s no conventional galvo scanning option, and since resonant galvos are not good for arbitrary line scanning, you’re pretty much locked into (fast) raster scanning. If that’s not an issue, it’s a good option. And I’m guessing they’ll have a conventional galvo scanning option at some point– they do actually sell them, all they have to do is integrate it into the software. Neither their software nor ScanImage 4 supports regular galvo scanning at this time, but at least the latter intends to add that functionality.
Josh Trachtenberg (UCLA) and his team has a new scope to offer. It’s a moving objective microscope in the same vein as the Sutter/Denk scope. This is an excellent team and they offer a well-designed scope. In particular, the scanning optics of this scope are very well thought out and designed. They also have a resonant scanning add-on with custom electronics. The following digrams are from an earlier version. They’re busy adding new features.
Till Photonics has a couple of systems on offer too. First up is the 2p version of their iMIC platform. These octagonal monoliths look like they should be launched into space.
Till Photonics’ modules are popular, particularly their Yanus scan head. The heart of it is a set of Cambridge Technologies 6210s, but they have them packaged up nicely in top quality optics and an easy-to-implement module. They have modelled the nonlinearities and can squeeze a bit more scan speed out of the mirrors if you use their systems.
Next up from Till is their Intravital 2p that came out this spring.
It boasts a fairly large scan field (about 15.5 mm to a side in the focus plane, divide by your objective’s magnification to get the field of view) and a voice-coil driven z-axis with 7.5 mm of travel.
By the way, Till Photonics runs Colibri, an open source, LabVIEW-based laser scanning microscope software package. It runs off of the NI PCI-6110 board that most people use. It’s modular, uses 4 MHz sampling, and has support for cameras, motor controllers, and beam control. So you don’t have to have a Till system to try out the software. The author, Christian Seebacher, has some interesting information about the software on his website.
I’m sure there’ll be more new stuff at SfN this year… let me know if you see anything interesting.
Sensapex is the new kid on the block for micromanipulators, and theirs have an ultra small footprint with 20mm of travel on 3 axes. Here are some pictures of one of the first production runs:
To change pipettes, the manipulators have a tilt-back action.
The tilt-back action should help conserve space in crowded setups, but the arc might not be clear. Some sort of sliding back and/or twisting motion might be needed.
They’re very small. Check out the Axon headstage next to them.
It’s really built to be a pipette holder-type manipulator rather than a larger, headstage holder-type manipulator. They have magnetic and bolt-on headstage mounting options for Axon, Heka, and npi.
They have a “high load” version that should handle 200g (the MultiClamp headstage is about 90g). So it should be possible to mount about any headstage directly on the manipulator. Having the headstage too far away from the pipette can cause noise problems, so this might be what people want to look for.
Here’s the controller:
They’re also considering releasing the user interface as open source. This is from Mikko, the CEO:
We are using PC-software in the R&D and testing, but we don’t yet have computer interface for the customers. We have had some requests for it though so it is in our R&D plan. However, we are happy to provide drivers, function calls etc. if someone wants to implement control to their existing software (Matlab, C or Labview based). I’ve been thinking of going for the open-source approach for the user-interface software.
Fun fact for the day: ThorLabs’ SM2 lens tube standard screws right onto the front end of Nikon’s SLR lenses. Other manufacturers probably use the same threading, I just haven’t tried them.
I don’t know if this is by design or not, but it makes coupling 35mm SLR lenses into optical setups fairly straightforward. I’m using it for a tandem lens macroscope. In the picture above I used ThorLabs part SM3A2. BTW, they also sell some F-mount adapters for connecting to the other side of the lens.
One of Josh Trachtenberg’s rules that I have adopted is “No Homemade Cables”. It’s so natural to think that this is the best solution to hook two things up: “Wire and bare connectors are so cheap, let’s just make our own cables.” However, homemade cables, even when made with great care, are usually of poor quality compared to commercial cables. As a result, you’re just giving yourself something else to repair in the future.
Adapter boxes, aka breakout boxes, are more reliable than homemade cables. If you take this route, put it in a transparent, easy to open box so that you can quickly see (a) how things are wired up, and (b) whether there are any loose connections.
Another option is to have custom cables made. I started doing this in London for a rig where I needed two fairly long 48-conductor cables. Custom cables are actually not that expensive and are of very high quality. It’s practical because you don’t have to buy an entire spool of 48-conductor wire (or whatever the job requires); nor do you have to source obscure connectors, strain reliefs, jackets, and whatnot. Not to mention time saved soldering.
Here are a couple of places that you can get quotes from if you’re interested. Any of them will do one-off jobs, you don’t have to bring them volume jobs.
Circuit Assembly
Technical Cable Concepts
Custom Cable Assemblies
Fritzing is PCB design software (EDA) in the spirit of Arduino and Processing. It’s open source, cross-platform, streamlined, and simple to use. It doesn’t do simulations, but you can lay out your circuit in a GUI that looks like a prototyping board, then move to circuit layout, and finally PCB design. Check out the video above to get an idea of the workflow of Fritzing.
PCB manufacturing is something that I haven’t covered in Labrigger before. Partially because I didn’t think there were good free software tools to use. I’ve used proprietary stuff in the past (Tanner EDA, due to my background in MEMS), and the free (as in beer, not speech) version of EAGLE is popular. But most of the GNU-licensed PCB design software was not quite ready for primetime in my opinion. Fritzing is the first thing I’ve seen that is really well done and has the potential for wide adoption.
Anyways, now that Fritzing is here, it’s worth mentioning how affordable it is to have a custom board house make your custom PCB. It’s so cheap, I really don’t recommend making PCBs at home or in the lab, although there are plenty of ways to do so. This isn’t anything new, cheap custom PCBs have been available for decades, but not a lot of people who make their own gadgets in biomedical research know how easy it is.
Fritzing has their own fabrication, named Fritzing Fab. They’re based in Germany. But Fritzing will output files that you can send to other board houses. A Google search for “custom PCB” will return a hot mess of hits. I recommend you look for one in your geographical area. If you’re in the US, this list is a good start. I’ve used Advanced Circuits before, but any of these firms are probably solid.
If you’ve got more than 20 interconnects to do, then it’s probably worth making a PCB. However, if you’re really unsure of your design and might need to make several changes, then maybe the threshold should be closer to 30 interconnects. Because although PCBs can be minimally modified (cutting traces, making jumpers), they’re harder to change.
Turn around time is another consideration. Custom PCB houses are built for short turn around, but they’re still 1-5 days, typically. So if you need it right now, you’re better off wiring it yourself. Especially if there is a low number of interconnects.
BTW, Fritzing is selling some nice Arduino kits as well (link).
More materials…
A video where Fritzing is used for a slightly larger circuit design
Labrigger posts on Arduino
Let me add some clarification to the hybrid PMT post.
The actual signal that comes off of a PMT in response to a photon is a pulse of current. The amplitude of this pulse can vary wildly, and the variation is referred to as multiplicative noise. For that reason, photon counting schemes typically use a simple threshold-crossing to trigger counts, which often mostly solves multiplicative noise. You’re smart, so I know you’re already wondering what happens when two pulses occur very close to each other in time. This is called “pile up” and it’s a problem. There are different ways to deal with it, but since single pulses can be so variable, it’s difficult to deal with it effectively. I also want to note that even for dim images, events WILL come close enough together SOMETIMES. And for bright images, it happens quite often, and this precludes quantitative imaging.
Hybrid PMTs address this by having a huge gain at the first stage which essentially decreases the noise (by a factor of sqrt(n)) so that the photon-evoked pulses are less variable. They can also be designed to make the pulses briefer. Brief pulses = less pileup, and more regular pulses means that more sophisticated schemes can be used to accurately count photons. All in all, this results in more quantitative imaging. Of course, this is most relevant for bright images.
Alright, back to watching Plaxico Burress not catching passes.
Hybrid PMTs have made their way into fluorescence microscopy and are competing with GaAsP PMTs. (Well, actually, Hamamatsu makes both types, so it’s not really competition in that sense.) These devices have a huge gain at the first stage, which results in lower multiplicative noise. But does it matter? And is it worth the trade off (e.g., some hybrids have smaller detector areas compared to GaAsP PMTs)?
This was the topic of a few recent (and long) posts on the Confocal Listserv. If you’re into this sort of thing, they make a great read.
James Pawley’s post
George McNamara’s post
Wolfgang Staroske’s post
The take-home message is that hybrid PMTs will keep you in a more linear range for bright images.
Some people have noticed higher S:N when they upgraded to hybrid PMTs. But without knowing what their old PMTs were, it’s hard to say that they can offer better images than a top-of-the-line, non-hybrid GaAsP PMT. Your milage may vary and all that. In any case, for dim images, there’s probably not much of an advantage. But for bright images, Hybrid PMTs can offer more quantitative images.
This all is most relevant in photon counting mode. Hybrid PMTs give less variable signals in response to single photons because of the high gain in the first stage.