A Clear Solution: Seeing living brain cells fire signals at high magnification by matching the refractive index between tissue & lens
📹 Shigenori Inagaki et al @imailab.bsky.social, Kyushu University in @natmethods.nature.com
➡️ bpod.org.uk/archive/2026... with
@rooph.bsky.social
SeeDB-Live is a tissue-clearing approach for live tissue slices or brains, improving image quality while having minimal effects on electrophysiological properties of neurons. @imailab.bsky.social
www.nature.com/articles/s41...
A step-by-step protocol has been posted in SeeDB Resources:
sites.google.com/site/seedbre...
The reagent will soon be commercially available from Nacalai Tesque.
www.nacalai.com/global/index...
We hope that our new tool will spark new applications in bioimaging!
(10/10)
We are grateful for the invaluable help from our collaborators.
More stories behind our findings:
Research Briefing: www.nature.com/articles/s41...
EurekAlert!: www.eurekalert.org/news-release...
The Transmitter: doi.org/10.53053/EIM...
(9/10)
We also successfully cleared the cerebral cortex of live mice. The brightness was 3x higher in L5. Sensory responses remained unchanged. We also established chronic imaging using a repeated clearing protocol, without any obvious inflammation or behavioral abnormalities. (8/10)
SeeDB-Live enabled us to perform 1P functional imaging of brain slices.
This movie shows 1P voltage imaging (Voltron2) of back-propagating action potentials in mitral cell dendrites, captured with a high-speed CMOS camera at 2 kHz. Single shot, no averaging. (7/10)
SeeDB-Live is useful for functional imaging of brain slices. This movie shows 2P imaging of GCaMP6f in mitral cells during the clearing of an olfactory bulb slice. Spontaneous activity was more clearly visualized after clearing, while the firing pattern remained unchanged. (6/10)
Using patch-clamp recording, we confirmed that neuronal firing properties remain largely unchanged after clearing. This was a tough experiment, because neurons become invisible after clearing. Nao Nakagawa-Tamagawa worked very hard to patch invisible neurons in cortical slices! (5/10)
To minimize osmolarity, we screened high-MW chemicals and found that BSA has an exceptionally low osmolarity. After fine-tuning the ionic compositions, we established a live tissue clearing agent, SeeDB-Live. The movies show the clearing of a HeLa cell spheroid. (4/10)
Similarly, live cells become transparent when immersed in a medium with the same refractive index (1.36-1.37). However, existing clearing agents have prohibitively high osmolarity and toxicity, precluding their use in *live* imaging of normal cellular functions. (3/10)
The principle of optical clearing is simple. When the refractive index mismatch is minimized, the light travels uniformly and samples become transparent. For example, glass marbles with a refractive index of 1.52 become transparent when immersed in oil with the same index. (2/10)
Our live tissue clearing paper is out in @natmethods.nature.com! We achieved optical clearing of mammalian brain tissues without compromising normal neuronal function. Big congrats to Shigenori Inagaki and our wonderful collaborators! 🎉
www.nature.com/articles/s41... (1/10)
Join us at TENSS 2026 to open black boxes, explain how things/brains work and debate the impact (or lack or it) of various new technologies on understanding of the brain and on society. tenss.ro Apply by: March 15th!
Our research on magneto-sensitive fluorescent proteins and some of their applications has now been published!
Huge thank you to the many many people involved in making this happen. 🧪
www.nature.com/articles/s41...
#ELMI2026 will take place in Coimbra, Portugal 🇵🇹from June 16-19 hosted by @ppbioimaging.bsky.social colleagues. Submit your abstracts for oral presentations by January 18!
More information & registration🔽
ppbi.pt/wordpress/in...
This is the result of the long-term efforts by Ryo Egashira and Meng-Tsen Ke, as well as our fruitful collaboration with @tsuyomiyakawa.bsky.social and Nao Nakagawa-Tamagawa. Congrats to the authors! (6/6)
L5 neurons are known to integrate sensory inputs to basal dendrites and top-down inputs to the apical tufts. The newly formed spines in the apical shaft may be critical for regulating dendritic integration. Also, dendritic integration in L5 may be affected by schizophrenia. (5/6)
We also found that mutations in schizophrenia-related genes impair adolescent spine formation, suggesting that spine formation in this specific dendritic compartment during adolescence is critical for the maturation of normal cognitive functions. (4/6)
It is well known that the “average” spine density in the cortex decreases during adolescence. However, we found that spine density in the middle part of apical dendrites greatly increases during adolescence. This contrasts with basal dendrites, where spine density reduces. (3/6)
Using tissue clearing and super-resolution imaging, we found that spine density is highly skewed in apical dendrites of cortical L5 neurons in mice. The middle part had the highest spine density. In contrast, spine density was almost uniform in basal and oblique dendrites. (2/6)
Our new paper is out in Science Advances! We found that dendritic compartment-specific spine “formation” during adolescence is critical for cortical development. We also found that schizophrenia-related genes are important in this process. (1/6)
www.science.org/doi/10.1126/...
In June 2001, I arrived in SFO with a suitcase, a student visa, and disproportionate dreams.
My life since has been nothing but a dream.
My heart is with the international students in the US today.
Our new paper is out in Science.
What is the synaptic plasticity rule in the brain, we asked. It turns out there are multiple, even within individual neurons.
Congrats Jake!
www.science.org/doi/10.1126/...
✨New paper from my lab out now in @cp-cell.bsky.social!
We identified pathways for airway protective reflexes—swallowing and coughing—in mice, driven by rare throat chemosensory cells that signal vagal nerves via channel synapses.
cell.com/cell/fulltex...
If you are interested in what happens deep in the brain during puberty, please check our new paper in Neuron. We visualize how nutritional status shapes sexual maturation in female mice: A flagship study by an excellent postdoc Teppei Goto. (1/N
How does neural activity control developmental synapse elimination? Here is a new review paper from the lab: Activity-dependent synaptic competition and dendrite pruning in developing mitral cells.
www.frontiersin.org/journals/neu...
A background in physics, and his own curiosity, have helped Dmitry Rinberg tackle the complexities of the neuroscience of smell. More on Rinberg sniffing out the mysteries of olfaction.
By Lina Zeldovich
www.thetransmitter.org/olfaction/sn...
The sympathetic nervous system may control selective organs, but how this specificity is achieved is unknown. Our new study
@NatureComms www.nature.com/articles/s41... uncovers a parallel labeled-line organization within the lower thoracic spinal cord. 1/
We also made a linear unmixing plugin for ImageJ/Fiji. You can use a conventional confocal for 7-color imaging: github.com/daichimori/L...
Paper: www.nature.com/articles/s41...
Additional codes at Github: github.com/TakeshiImaiLab
Addgene: www.addgene.org/Takeshi_Imai/
