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filipjaniak.bsky.social

@filipjaniak.bsky.social
225 followers 276 following 11 posts

Building tools for neuroscience: optical instrumentation, multiphoton microscopy, custom hardware, 3D printing and open science

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Lukas Groschner @lukasgroschner.bsky.social · 29/09/2026
Single-neuron computations depend on the subcellular distribution and voltage sensitivity of ion channels. | @pnas.org #HorizonEU @erc.europa.eu (1/5) www.pnas.org/doi/10.1073/...
pnas.org
Distribution and voltage dependence of ion channels shape single-neuron computations | PNAS
Voltage-gated ion channels do not distribute evenly in the plasma membrane of a neuron; they localize to distinct domains where they govern the exc...
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Takuya Sasatani @takuyasasatani.bsky.social · 14/09/2026
Miniscope Zero, the first fully wireless Miniscope, is on @biorxivpreprint.bsky.social! Wireless power + data enable neural recordings in enclosed mazes, 3D environments & from two animals at once! @miniscope.bsky.social Paper: doi.org/10.64898/202... Wiki: miniscope.org/wiki/Minisco...
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Nature Methods @natmethods.nature.com · 05/08/2026
An Analysis from @ptrrupprecht.bsky.social et al investigates the behavior of GCaMP8 variants in spike inference using different algorithms. www.nature.com/articles/s41...
nature.com
Spike inference from calcium imaging data acquired with GCaMP8 indicators - Nature Methods
In this Analysis, Rupprecht et al. investigate the behavior of GCaMP8 variants in spike inference using several different algorithms. They highlight the role of the indicators’ linearity in the infere...
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filipjaniak.bsky.social @filipjaniak.bsky.social · 05/08/2026
Interesting follow-up to our nTC work: Na Ji’s group shows that extending the axial PSF can bias ΔF/F, response classification, tuning and correlations in 2P calcium imaging — a strong reminder to match the PSF to the biological scale, not just the desired FOV. www.biorxiv.org/content/10.6...
biorxiv.org
High Axial Resolution Is Necessary for Quantitative Two-Photon Calcium Imaging of Neuronal Populations
Two-photon calcium imaging is a standard tool for measuring neuronal population activity in vivo , yet how axial resolution, sensor expression strategy, and analysis pipeline jointly affect data accur...
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George Kafetzis @gkafetzis.bsky.social · 25/07/2026
Curious about sharks? The evolution and adaptation of vertebrate visual circuits? 🦈 🐟 🐤 🐁 👁️ I'll be speaking at ICN2026 @neuroethology.org on Friday, or just find me to chat! Special thanks to @anna-stoeckl.bsky.social and Gregor Belušič for the wonderful session within yet another wonderful ICN!
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Nature Methods @natmethods.nature.com · 23/07/2026
FlatMux: an optimized microscope system for multiplexed 2-photon imaging of neuronal activity with voltage sensors. www.nature.com/articles/s41...
nature.com
A versatile platform for two-photon neuronal population voltage imaging across cortical depths - Nature Methods
FlatMux is an optimized microscope system for multiplexed two-photon imaging of neuronal activity with genetically encoded voltage sensors. The flexible system is demonstrated in a variety of scenario...
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Dominic Gonschorek @dgonschorek.bsky.social · 23/07/2026
Excited to see the OpenRetina project out! 🚀 A collaborative framework for training, benchmarking, and interpreting retinal neural network models across datasets and species. If you work in computational neuroscience, vision, or ML, check it out. We'd love to see the community use and extend it. 👁️🤖
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adamezracohen.bsky.social @adamezracohen.bsky.social · 20/07/2026
We developed a new approach for mapping absolute membrane voltage, based on dynamic photocycle control in Voltron2. www.biorxiv.org/content/10.6... Here's my favorite example: human iPSC colonies break into electrical domains as they begin to differentiate.
Top image shows a greyscale picture of some cells.  Bottom image shows a voltage map overlay in color, with two electrical "domains".Wide-area view of membrane voltage in human iPSC colonies.
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Alfred Millett-Sikking @amsikking.bsky.social · 20/07/2026
Ultrafast 3D imaging just got faster! Introducing: "Instant dual-view Snouty (iDV-Snouty) light-sheet microscopy" -> Double the data rate of a Snouty microscope by adding a 2nd view! Use the extra view for a variety of imaging modes! Article here: amsikking.github.io/idv-snouty_l...
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Ivan Manzini @xenofrog.bsky.social · 07/07/2026
🐸 Postdoc Position (m/f/d) in Neurobiology! The project focuses on how smell shapes feeding behavior in poison frogs and is conducted in collaboration with Prof. Jennifer Stynoski (Costa Rica). 🌎🌿 . For more information and to apply, please use the link below. www.uni-giessen.de/de/ueber-uns...
uni-giessen.de
Research Associate / Postdoctoral Researcher (m/f/d) “Olfactory Control of Behavior in Amphibians”
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Michi Forsthofer @mforst.bsky.social · 06/07/2026
Corporate wants me to find the difference between these pictures. If you too want to know how brains reprogram during metamorphosis, come to my poster at #FENS2026 Tuesday morning
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Ian Oldenburg @ianoldenburg.bsky.social · 30/06/2026
Really excited to share our new preprint. Here we use our holographic optogenetics to ask a key question about how neurons need to fire to drive movements. We find a bunch of interesting things about what does, and doesn't drive movements. Brief summary below www.biorxiv.org/content/10.6...
biorxiv.org
The Importance of Synchrony in the Neural Control of Movement
Throughout the mammalian cortex, populations of neurons must work together to enact behaviors. While population recordings in motor cortex have revealed many aspects of when neurons fire during behavi...
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Horst Obenhaus @octoscience.bsky.social · 29/06/2026
🌟 NEW OCTRON RELEASE! 🌟 Want to track your animals using the command line? You can now train models and predict videos with single prompts in a terminal! Ideal for batch jobs, headless servers, and remote machines. Big shout-out to @roald-arboel.com for helping with this release!
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Jonas Wietek @jwietek.bsky.social · 08/06/2026
A red-emitting, genetically encoded indicator for two-photon voltage recording in vivo www.biorxiv.org/content/10.6...
biorxiv.org
A red-emitting, genetically encoded indicator for two-photon voltage recording in vivo
Genetically encoded voltage indicators (GEVIs) enable minimally invasive, cell‑type‑specific optical measurements of neuronal membrane potential with millisecond temporal resolution. Red‑shifted GEVIs...
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James Manton @jamesdmanton.bsky.social · 02/06/2026
We present: Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution www.biorxiv.org/content/10.6...
Image of first two pages of manuscript.
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David Vijatovic, PhD @neurodave.bsky.social · 02/06/2026
Excited to share that the main project from my PhD is now out in @cp-cellreports.bsky.social! 📄 www.cell.com/cell-reports... @istaresearch.bsky.social
cell.com
Multifold increase in spinal inhibitory cell types with emergence of limb movement
Frog metamorphosis reveals how spinal circuits adapt to new motor demands. Vijatovic et al. demonstrate that the shift from tail- to limb-based locomotion coincides with expansion and diversification ...
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Tom Baden @neurofishh.bsky.social · 29/05/2026
Delighted that a new online talk is up for viewz on Youtube: "Evolution of the Vertebrate Eye". Thanks to Marion Silies and Luisa Ramirez for hosting! www.youtube.com/watch?v=BrYJ....
youtube.com
Tom Baden - Evolution of the Eye
YouTube video by BadenLab
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Pranav Seth @thebuddhabird93.bsky.social · 22/05/2026
#FluorescenceFriday ✨ A glimpse into the beautifully layered architecture of the zebra finch retina highlighting the remarkable stratification of retinal cells and circuits from two different perspectives: 🔬 First image: a side view
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UCSB Electrical and Computer Engineering Department @ucsbece.bsky.social · 18/05/2026
🔬How do you study thousands of neurons at once? You build better tools. ECE Prof. Spencer Smith's SLAB Lab designed a scan angle multiplier that achieves the laser scanning trifecta: high speed, high resolution, and a larger area.🧠⚡ 📜https://tinyurl.com/36j7pa3d
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Tom Baden @neurofishh.bsky.social · 06/05/2026
How is the ON and OFF pathway split in the visual system? 🤔 The textbook standard, that bipolar cells are separated simply by the glutamate receptors they express, might be due for an update....a short 🧵
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Ryan Fink @finkryan.bsky.social · 24/04/2026
PinkyCaMP is finally published!! My first paper co-first authored with @sikmys.bsky.social where we make a great optogenetic and multiplex compatible red calcium indicator. Thank you to @massecklab.bsky.social and @campbell-lab.bsky.social for guiding this journey www.nature.com/articles/s41...
nature.com
PinkyCaMP: an mScarlet-based calcium sensor with enhanced brightness, photostability and multiplexing capabilities - Nature Methods
PinkyCaMP is a red genetically encoded calcium indicator with improved brightness and photostability. Derived from mScarlet, it does not exhibit photoswitching upon blue light illumination and is ther...
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Andre M Chagas @iamchagas.bsky.social · 23/04/2026
Beehive's #preprint is out! A simple electronics platform platform for building research tools and to teach programming.. preprints.scielo.org/index.php/sc... #openhardware #neuroskyence
preprints.scielo.org
BeeHive: A flexible open electronics platform for controlling research equipment and teaching electronics principles
In this manuscript we present BeeHive, a standardized, open-source hardware electronics ecosystem designed to address challenges faced by researchers when developing custom scientific equipment. Beehive is flexible and interoperable, since it is organised around minimal design rules. It consists of a microcontroller-based mainboard and function-specific Daughter Boards (DBs) for controlling actuators or reading sensors, allowing researchers to rapidly combine and repurpose components to build complex, specialized systems. This modular approach significantly reduces the time and cost associated with instrumentation development, promoting effective collaboration through shared, standardized solutions. The platform's versatility is demonstrated across several neuroscience applications, including a reward delivery system for head-fixed mice, a modular mouse maze, and an odour stimulator, alongside a dedicated Training DB and curriculum designed to teach electronics and MicroPython programming in an integrated, project-based manner. By embracing open-source principles for hardware and software, BeeHive lowers the barrier to entry for researchers in developing their own setups, fostering greater accessibility, reproducibility, and innovation. The system is also discipline agnostic, and could be used to create tools in different fields.
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Anna Vlasits @annaintegrated.bsky.social · 16/04/2026
The Vlasits Lab is hiring a technician because our current technician was accepted into a PhD program! This position combines lab management and experiments. If you are interested in gaining experience with #retina research in Chicago, please apply. vlasitslab.org uic.csod.com/ux/ats/caree...
vlasitslab.org
Vlasits Lab
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Tom Baden @neurofishh.bsky.social · 21/04/2026
International Colour Vision Society (ICVS) Conference coming up here in Brighton August 14-18 2026. Abstracts open till mid May. www.icvs2026.org! 🌈 🌊 🐬 ☀️
icvs2026.org
ICVS2026
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Nature Methods @natmethods.nature.com · 16/04/2026
New voltage indicators JEDI3sub and JEDI3hyp allow monitoring subthreshold neuronal activity in awake mice. @stpierrelab.bsky.social www.nature.com/articles/s41...
nature.com
Designer indicators for two-photon recording of subthreshold voltage dynamics - Nature Methods
The genetically encoded voltage indicators JEDI3sub and JEDI3hyp enhance monitoring of subthreshold neuronal activity in the awake mouse brain using a variety of two-photon microscopy techniques.
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Pranav Seth @thebuddhabird93.bsky.social · 03/04/2026
Looks like a cosmic explosion… but it’s actually a #zebrafishretina 🔬 Pancone line expressing syGCaMP6f Confocal, whole-mount prep Sometimes biology doesn’t need enhancement to look spectacular. #FluorescenceFriday #Neuroscience #Retina
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Katrin Franke @katrinfranke.bsky.social · 31/03/2026
New paper out in @cp-neuron.bsky.social 🎉 What determines contextual modulation in V1? Why does the visual surround sometimes facilitate and sometimes suppress a neuron's response to its preferred stimulus?
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Tom Baden @neurofishh.bsky.social · 31/03/2026
FASEB Retinal Neurobiology: Celebrate 30+ years of research on cellular and molecular mechanisms that drive vision, retinal function, and degeneration. Join keynote Massimo Scanziani alongside organizers Wei Li and Wei Wei. Submit your abstract by April 13 and register now: hubs.ly/Q047K6gk0
hubs.ly
Home - Retinal Neurobiology and Visual Processing.
Join vision scientists and neurobiologists to explore retinal development, disease, and repair, with insights into visual processing and disorders.
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Ferenc Mueller @ferencmueller.bsky.social · 27/03/2026
Uni Sussex ditto
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Ryan MacDonald @macdonaldlab.bsky.social · 03/03/2026
Excited to share our new manuscript from the Yoshimatsu and MacDonald labs. www.biorxiv.org/content/10.6.... We found that my favourite glial cells can regulate local retinoic acid signalling to specialise cone photoreceptors for high acuity visual function.
Muller glia (green) regulate local retinoic acid signalling to specialise photoreceptor outer segments (magenta)for high acuity visual function
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Tom Baden @neurofishh.bsky.social · 28/02/2026
Happy to see how our collab. paper on the origin of the vertebrate eye is tickling the public interest. Our ongoing shuffle from systems neuro to evo-neuro over recent years continues to be a delight! We are supported by various funders, but I want to point out one in particular: @leverhulme.ac.uk
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Thomas Nowotny @drtnowotny.bsky.social · 27/01/2026
Happy to share our preprint on ephaptic interactions between olfactory receptor neurons in Drosophila by Lydia Ellison. doi.org/10.64898/202... We set out to see how near-instantaneous electrical interactions are good for processing tiny odour onset delays, only to find that they weren't.
doi.org
History-dependent ephaptic interactions in paired olfactory receptor neurons
Olfactory sensing begins with the transduction of odors into receptor currents on the dendrites of olfactory receptor neurons (ORNs). In insects and many other arthropods, ORNs are grouped stereotypically in hair-like sensilla on the surface of olfactory organs, enabling mutual inhibition through non-synaptic 'ephaptic' interactions (NSIs). Given the electrical, and therefore virtually instantaneous, nature of NSIs, it has been hypothesized that they contribute to processing fast temporal elements of mixed odor plumes. Here, we present single sensillum recordings and computational modeling that characterize NSIs during short offset dual-odor stimulations in the olfactory sensilla of adult female Drosophila melanogaster. We find in the experiments that the magnitude of inhibition between co-housed ORNs cannot be predicted by their instantaneous activity (firing rate) alone. It is adaptation-dependent, with strong effects only occurring when the inhibited ORN is adapted. This limits the usefulness of NSIs for fast odor processing when ORNs lack time to adapt. We reproduced the observed phenomena in a computational model and use this model to explain how the adaptation-dependence of NSI-mediated inhibition arises from nonlinearities in neural responses. We conclude that NSIs are unlikely to support the encoding of fast temporal dynamics in mixed odor stimuli, instead contributing to slower peripheral processing, supporting roles such as novelty detection. More broadly, we demonstrate how the nonlinear interactions of fairly simple electrical components lead to non-intuitive results, offering insight into the longstanding debate around ephaptic interactions in other systems, such as the mammalian CNS. ### Competing Interest Statement The authors have declared no competing interest. Leverhulme Trust, https://ror.org/012mzw131, RPG-2019-232 Engineering and Physical Sciences Research Council, https://ror.org/0439y7842, EP/P006094/1, EP/S030964/1
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jakubcz96.bsky.social @jakubcz96.bsky.social · 14/01/2026
💎 New Publication Alert: Next-Generation Calibration Materials We propose fluorescent nanodiamonds as a superior alternative to standard beads for calibrating two-photon systems. Check out: www.biorxiv.org/content/10.6... #Microscopy #Science #Innovation #Photonics #AcademicPublishing
biorxiv.org
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filipjaniak.bsky.social @filipjaniak.bsky.social · 14/01/2026
1/10 New preprint on bioRxiv Nanodiamonds for spatial resolution benchmarking in two-photon microscopy We introduce nanodiamond-based phantoms as a robust, reusable alternative to bead–agarose samples for PSF calibration. www.biorxiv.org/content/10.6...
biorxiv.org
Nanodiamonds for spatial resolution benchmarking in two-photon microscopy
Reliable and reproducible measurement of spatial resolution is essential for validating and comparing the performance of two-photon microscopy systems. We present fluorescent nanodiamonds as robust, photostable, reusable, and biocompatible probes for benchmarking spatial resolution. Owing to their nanoscale dimensions and stable fluorescence, nanodiamonds act as near-ideal point-like emitters, enabling accurate characterisation of the point spread function across varying imaging conditions. We demonstrate that nanodiamond-based phantoms serve as a reliable alternative to conventional fluorescent beads embedded in agarose, while at the same time offering advantages in stability and optical properties. Our results position nanodiamond phantoms as a next-generation calibration material that bridges ease of use and reproducibility, advancing quantitative imaging and cross-platform comparability in modern fluorescence microscopy. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, https://ror.org/029chgv08, Investigator Award in Science 220277/Z20/Z European Research Council, https://ror.org/0472cxd90, ERC-StG “NeuroVisEco” 677687, ERC AdG “Cones4Action” covered under the UK’s EPSRC guarantee scheme EP/Z533981/1 UK Research and Innovation, https://ror.org/001aqnf71, BBSRC, BB/R014817/1, BBSRC, BB/W013509/1 International Human Frontier Science Program Organization, https://ror.org/02ebx7v45, RGP001/2025 Leverhulme Trust, https://ror.org/012mzw131, PLP-2017-005, RPG-2021-026, RPG-2-23-042 Lister Institute of Preventive Medicine Gdańsk University of Technology, https://ror.org/006x4sc24, Nobelium DEC-4/1/2024/IDUB/I.1a/No, Platinum 1/1/2025/IDUB/I.1B/Pt
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Simon Schultz @simonschultz.bsky.social · 10/01/2026
A new version of our 2p mesoscope paper is up on biorxiv: Yang et al, Ultra-wide-field, deep, adaptive two-photon microscopy. www.biorxiv.org/content/10.1...
biorxiv.org
Ultra-wide-field, deep, adaptive two-photon microscopy
Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain r...
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 12/01/2026
"These results show that spontaneous activity in the vertebrate brain is highly stereotyped at the level of functional cell assemblies and can be reliably captured through a common latent code." New work from Volker Bormuth Lab @sorbonne-universite.fr 🐟🧠
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