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Tools for Looking into the Brain: Fluorescence Microscopy

In this episode, we discussed the basic principles of fluorescence microscopy and how it can help us understand the brain. We explored how fluorescence can be targeted to specific cell types or cellular structures, and the different types of microscopes that can be used to image this fluorescence, from widefield to confocal to 2-photon microscopes! We also discussed the advantages of each microscopy technique, and explored some examples of research studies that have taken advantage of them.

Listen to the episode here

You can find Scientifica's blog post about this episode here.

For an excellent overview of fluorescence microscopy, check out this review by Lichtman & Conchello, 2005, or a more recent review by Sanderson et al. 2014.

For a more basic overview of fluorescence microscopy techniques, check out this website Microbe Notes.

Fluorescence microscopy relies on the excitation of fluorescent proteins or fluorophores by light or a laser beam of light and subsequent detection of their emittance of a different wavelength of light, which depends on the excitation/emission spectra of the fluorophore (image from

We also described how fluorescent proteins can be expressed in specific cells in the brain, or how specific proteins can be tagged with fluorophores so that they can ultimately be visualised. A very commonly used method for this is termed immunohistochemistry- you can learn more about it in this review article.

We also spoke about a novel kind of fluorescent reported that depends on an engineered transcription factor that, upon enough activity and thereby calcium influx within a neuron, leads to transcription of a fluorescent reporter, enabling high temporal precision in labelling increased activity of neurons. You can find the published paper here: "A light- and calcium-gated transcription factor for imaging and manipulating activated neurons" Wang et al., 2017

You can find a variety of articles focusing on each microscopy technique on Scientifica's website. Check them out below!

Widefield fluorescence microscopy

Multiphoton microscopy

We also highlighted a study that used two-photon microscopy to image neural activity in zebrafish during social behavior to uncover the underlying neural circuits. You can find the paper, entitled "Visual recognition of social signals by a tectothalamic neural circuit", by Kappel et al., 2022 here

...and mentioned the more recent advancement of three-photon microscopes that enable even higher resolution images to be taken deeper in neural tissue. Find the published paper here: A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice

This episode is part of a series sponsored by Scientifica, one of the leading producers of state-of-the-art electrophysiology and imaging tools. Scientifica supports researchers around the world to make advancements in neuroscience, cardiology, cancer research, and various other scientific areas. In addition to leading equipment and comprehensive support, Scientifica hosts an extensive Resource Centre dedicated to fostering the sharing of expertise, which is full of a wide range of blogs, videos, case studies, and much more! Be sure to check out their website for more information.

The image for the cover of this blog post was taken and provided by Dr Federica Riccio.


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