Creating tailor-made optical microscopes to non-invasively explore morphogenesis and function in living organisms.
FAQ
The concept
What is a Flamingo? The Flamingos are a family of state-of-the-art, configurable and portable light sheet microscopes. The instruments are designed to perform optimally for a given application and continuously evolve over time. We use modular components in the lab to adapt the system to the user’s needs. The performance is comparable to the technology we use every day in our lab, without sacrifice to image quality.
What is the Flamingo for?
We use the Flamingo as a tool to collaborate with scientists around the world. Rather than sending precious samples from one lab to another, we send Flamingos to the users so that they can stay where their experiments work the best.
Where did this idea come from?
We had many unique purpose-built light sheet microscopes in the lab that ended up employing incompatible hard- and software. With the Flamingo we achieve a standardization of the technology in our lab. We believe that there is more to be gained with many standard microscopes than a single super-duper-fancy-thang. We soon realized that this unified concept would be ideal for tailoring a microscope to a collaborator’s application. And as we were making this instrument smaller and smaller, the Flamingo was born!
Who will this benefit? Hopefully you and us. The Flamingo will strengthen the scientific community by providing a shareable research technology on a common hardware and software platform. It allows us to effectively engage in more frequent and more diverse collaborations with people all over the world. At the same time, we gain a more complete understanding of what microscope users really need, which makes us more effective than we would be simply fiddling around with optics in our basement.
What is the benefit to the community?
The Flamingo opens up a new way of thinking about how scientific and financial resources are provided and used effectively. By sharing our knowledge and instruments with the community more people get access to state-of-the-art imaging technology. Sharing microscope hardware is a powerful alternative to putting a single piece of expensive equipment with a narrow range of applications into a single lab.
What is the benefit to researchers?
The Flamingo concept will benefit you as a user if a temporary, non-commercial and free microscope is what you need for your research. Maybe you just want to test light sheet microscopy and do not want to buy a commercial system right away. Maybe your application requires a dedicated configuration that none of the commercial systems offer. Maybe you just need an instrument for a short period of time to take the data you need. The Flamingo is a microscope that is tailored to your application and can be further optimized over time in a dialogue with us. You get to specify your exact needs and you get access to a state-of-the-art instrument for a limited period of time to acquire the data you need.
What is the benefit for the Huisken lab? While still fundamentally advancing microscopy, through the Flamingo project we learn what biologists in the field really need. We will then hopefully be able to build more usable and useful microscopes. And, hey, it is a cool optics and engineering challenge to build a microscope that can travel to another lab…
How is the project funded?
The Flamingo project is funded by traditional grants and/or philanthropy endeavors. Funding efforts are ongoing.
How can I get involved? The project’s success relies on your support and involvement. So thanks for asking. If you are primarily a microscopy user, you can support us by collaborating with us with an exciting project (and then tell everyone how good the microscope is). If you are a technology developer, you are welcome to help us make the instruments better or more capable. For example, you can design an add-on that fits our modular scope or you can write software to analyze some of the data all these Flamingos produce. And, of course, you are always welcome to become a sponsor of the project.
Is this related to OpenSPIM?
OpenSPIM is a great introduction for scientists who want to build their own light sheet microscope. The Flamingo project is a state-of-the-art platform providing tailored light sheet microscope for builders and biologists alike and independent from the OpenSPIM project and not intended to replace it.
Is this an open source project? We are more than happy to share details about the software and hardware at any given time. However, it is our greatest hope that people do not focus on trying to copy the Flamingo in its present form, but that what is learned from our projects successes and even its failures will contribute to better tools and new ways to share them for light sheet, for microscopy and maybe even beyond. The project’s focus is sharing our Flamingos widely across many individuals, institutions and regions and therefore the instruments are purpose-built to be traveling sharable instruments. There is no single Flamingo we could give you the plans for, as it evolves over time and from application to application. We are not even confident that our current approach is the best and we need the user’s feedback to figure it out. We do not want to encourage people to build a snapshot of this process that may then fail to meet the high standards and the philosophy of this project.
Logistics
How do you determine who gets the microscope? We are looking at a few different criteria before we engage in a new collaboration. Most importantly, we need to be convinced that the project is actually feasible with our technology. Secondly, we are looking to do great, impactful and innovative science in these projects. And lastly, we also want to be challenged such that the collaboration will drive the microscopy development forward.
How long can I keep the microscope for?
This will certainly depend on the project, but we plan to leave the Flamingo up to 3 months with you. It can be requested again if reviewer #3 asks for more data.
Can I keep the microscope if I like it?
We are pleased if your experiences have been positive. However, this is a non-commercial initiative and we want Flamingos to be permanently updated and improved, and therefore never outdated. You cannot domesticate a Flamingo.
Is there any cost associated?
You will have to provide your own data storage. This and your time are your commitments in this collaboration. We may also have the user cover shipping costs.
Will someone come to install the microscope for me?
You shouldn’t need any help setting up the microscope, it will be an easy process. However, in some areas where there is a need for many Flamingo installations we may have staff on site to assist with experiments.
Is training provided? Yes. We offer workshops where you get to learn how to use the microscope when it arrives in the mail.
What if something breaks?
Let us know. We want to fix it and improve these components.
Is there a geographical area covered?
We are starting to launch the Flamingo in the US, simply due to logistical reasons. We will expand the project worldwide as the project gets going.
Do I retain full rights to the data collected?
Yes. We ask you to give us feedback about the performance of the instrument you have used and to include us as co-authors on resulting publications.
Technical
Will this work for my sample? This is exactly where the Flamingo excels: Just try it out! We will have a database of previous cases and hopefully gain experience with even the most exotic samples.
How long can I image my sample for?
Since the phototoxicity of light sheet microscopy is relatively low, the duration of a timelapse mostly depends on the embedding. Ultimately, the main challenge is to maintain the sample’s health in the microscope during an extended period of time.
How many colors can I image?
All major fluorophores are supported, There is no difference to other fluorescence microscopy techniques. The same limitations apply, e.g. regarding spectral overlap of adjacent fluorophores, dye density, transgenes, etc. Typically you can image 2-4 colors simultaneously.
What is the spatial/temporal resolution?
The spatial resolution is given by the chosen lens and the pixel size of the camera. In light sheet microscopy you have the additional advantage of optical sectioning over the widefield microscope; you get better contrast with superior dynamic range and less photodamage than in the confocal. The frame rate of the system and the number of planes per second is typically 40 – 400 (depending on the number of pixels).
Is environmental control possible?
We are working on it and need to learn about the needs of your application (temperature/gases etc.).
What functionalities are there?
ll All Flamingos are capable of capturing ultra-high-speed single plane movies, fast 3D stacks in multiple colors and timelapses. Some configurations allow multi-view imaging by sample rotation or by using additional sets of lenses for illumination and detection. Multiple areas can be imaged sequentially and in several samples in series. The light sheet is generated with cylindrical lenses and pivoted with a galvo mirror to reduce shadowing. We are working on a version for cleared tissues. The main lens configurations are L (1 ill, 1 det), T (2 ill, 1 det), X (2 ill, 2 det), V (1 ill, 1 det dipping into dish), iV (1ill, 1 det, inverted, from below).
How do I know which configuration best fits my needs?
We will tell you from our experience and other users’ experiences. Maybe you already have found a light sheet reference where someone has used a particular configuration. Generally, the L, T, X configuration are great for most embryos, plant roots, cleared tissues, etc. The V configuration is used for samples in a dish such as multiple embryos spread out in a grid, flat tissue sections or 2D cell cultures. The iV-configuration has been used for particularly delicate samples that otherwise defy usual embedding or to provide easy access to the sample.
To what degree is the performance compromised?
The Flamingo is a state-of-the-art light sheet microscope that is just as good as other systems in the Huisken Lab. Paired with an appropriate data storage solution, the achievable frame rate and sample throughput can be maximized.
Is the Flamingo better than a commercial microscope?
It is certainly more adaptable and this may make the difference in your application.
How large a sample can I image with the Flamingo? This depends largely on the optics (magnification, working distance). We currently support samples up to ca. 5-6mm in thickness. Depending on transparency of the sample, tissues as deep as 500 µm can be imaged. The Flamingo for cleared tissues will allow deeper tissue imaging still (up to a cm) and accept larger samples.
Can I build my own sample chamber/add on? We invite you to make improvement suggestions and will adjust the microscope for your needs.
How much data does the microscope produce and is storage provided? The microscope can easily produce TBs of data. However, you can also run the microscope at reasonable speeds while still collecting sufficient data and without exhausting typical storage solutions. . A single image is typically 8MB, a single stack a few GBs. The microscope does not come with any storage. You will need to provide a storage solution (local or via network). We help you find the right solution.
How do I process and analyze the data?
You can use any image analysis software you may already be familiar with: ImageJ, FIJI, other (LSFM specific) open source tools, Aivia, Imaris, Amira, etc.
