Fabrizio Musacchio

@fabmusacchio

Physicist by training, working in computational neuroscience at the @dzne.science. Interested in how neural dynamics and learning shape brain function and behavior, using modeling and data analysis. 🌍fabriziomusacchio.com 🐘mastodon.social/@FabMusacchio

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Fabrizio Musacchio@fabmusacchio· 2d

🚀Another #MotilA update this morning: v1.1.3 brings optional #CSV & #YAML export, which makes MotilA less reliant on proprietary file formats. … And: MotilA got its first logo 🤗 🌍 motila.readthedocs.io/en/latest/ch... #BioimageAnalysis #microglia #motility #Python

A smiling cartoon cell with colorful extensions and the text "MotilA" below, representing a Python-based image analysis pipeline.

Fabrizio Musacchio@fabmusacchio· 3d

One thing that surprised me: I don’t see Roth’s #HST work on #Europa’s #plume/water-vapor signatures cited here, nor Saur et al. or much from the Europa #SpacePlasma community. Not fatal for their thermo-fluid model I guess, … #IcyMoons #SpacePhysics

Source: https://umbertogaetani.substack.com/p/il-guscio-di-ghiaccio-di-europa-potrebbe

Fabrizio Musacchio@fabmusacchio· 3d

If correct, shallow liquid reservoirs on #Europa may form more by local in situ melting than by direct #ocean-to-surface exchange. #PlanetaryScience #SpacePhysics #IcyMoons

This artist's concept depicts NASA's Europa Clipper spacecraft as it orbits Jupiter and passes over the gas giant's ice-covered moon Europa. Scheduled to arrive at Jupiter in April 2030, the mission will be the first to specifically target Europa for detailed science investigation. Credit: NASA/JPL-Caltech

Fabrizio Musacchio@fabmusacchio· 3d

🚀 #MotilA now runs with #OMIO! v1.1.2 adds much more flexible image I/O: #TIFF/ #OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO & normalized to TZCYX axis-order, automatically. No more manual axis reordering before analysis🤗 🌍 motila.readthedocs.io/en/latest/ch... #microglia #motility

Screenshot of MotilA documentation page with images illustrating segmentation and microglial turnover rate analysis.

Fabrizio Musacchio@fabmusacchio· 3d

#OMIO is meanwhile at v0.2.9 🚀 Main focus last week was making #Thorlabs RAW handling more robust: Better #XML/ #YAML #metadata fallback, support for batch-friendly error handling, & clearer diagnostics when metadata doesn’t match the data. 🌍 omio.readthedocs.io/en/latest/ch... #BioimageAnalysis

Fabrizio Musacchio@fabmusacchio· 3d

Nice little guide on how to read #maths by @petraschwer.bsky.social: 🌍 doi.org/10.48550/arX... I especially like the reminder that reading #mathematics is also #writing. That’s what distinguishes it from 👓 a novel: understanding comes from working through the material, not just reading over it.

Fabrizio Musacchio@fabmusacchio· 7d

…During pursuit, sweeps narrow & track a moving target; after sudden target changes, they reorient before the 🐀 turns; during backward locomotion, they reverse; even during #REM💤, sweep structure is modulated. …

Fabrizio Musacchio@fabmusacchio· 7d

This is the exciting part: #KHI can mix magnetized and non-magnetized #plasma, drive #turbulence, transport mass/energy/momentum/ #MagneticFlux, and may contribute to small-scale #magnetic braiding, thus one route by which free #MagneticEnergy is built up in the solar #atmosphere. #SpacePhysics

Fig. 1: A view of the solar photosphere at a spatial resolution of 19 km.

Fig. 2: Overview of the MURaM simulation.

Fig. 3: Observed versus synthetic KHI vortices.

Fig. 4: Temporal evolution of the KHI in the MURaM simulation, rendered with the VAPOR code

Fabrizio Musacchio@fabmusacchio· 8d

See how much #dendritic geometry matters for #SpatialCoding: clustered excitatory inputs on #CA1 #dendrites can support stable #PlaceFields with fewer active #synapses, by engaging local nonlinearities and Ca2+ signaling:

Fabrizio Musacchio@fabmusacchio· 11d

For those at #UniBonn & affiliated institutions: A TRA workshop on "Great Data – Great Science" will be held on Oct 6, covering #ResearchDataManagement, #DataScience, #HPC, #OpenScience, & related topics. ⏰ Abstracts: Sep 15, 2026 📍 Wissenschaftszentrum #Bonn 🌍 indico.hiskp.uni-bonn.de/event/1445/

Fabrizio Musacchio@fabmusacchio· 12d

Great step 🇪🇺 💪 PS: Their Marstodon Post is even funnier 🐘 https://ec.social-network.europa.eu/@EUCommission/117024814378891853

Fabrizio Musacchio@fabmusacchio· 15d

Today’s release of #OMIO v0.2.6 is again a small update, but brings memory-efficient OME-TIFF writing for Zarr-backed workflows. When imwrite receives a disk-cached #Zarr array, OMIO now streams it plane by plane instead of materializing the full store in RAM. 🌍 omio.readthedocs.io/en/latest/ch...

Fabrizio Musacchio@fabmusacchio· 17d

#OMIO is now at version v0.2.4. This maintenance release brings cleaner API docs, disk-backed empty image creation, and a more convenient #napari opener with automatic layer names, custom channel labels, and configurable blending ✌️ 🌍 omio.readthedocs.io/en/latest/ch... #BioimageAnalysis

Fabrizio Musacchio@fabmusacchio· 18d

Best part: The debut of "the polyclonals", a real #Bonn Science Band made up of #BfB members 🎸🤟 Hopefully, we’ll see and hear them again next year 🙏 #BonnerForumBiomedizin #Neuroscience

Fabrizio Musacchio@fabmusacchio· 18d

#BfB summer party in the #BotanicalGardens of #UniBonn last Thursday! Apart from a nice BBQ and cold drinks, there was plenty of time for good conversations with colleagues from the #Bonn #biomedical community 👌 #BonnerForumBiomedizin (https://www.bfb.uni-bonn.de/en)

Fabrizio Musacchio@fabmusacchio· 19d

Sunday reflections. #Cologne #July 2026 #WeekendStories #Nofusion

Shot with No Fusion by "NC".
A cozy, cluttered workshop with a guitar, workbench, plants, and various tools, seen through a glass window with a blurred reflection.

Fabrizio Musacchio@fabmusacchio· 24d

And if you are interested, I wrote a simplified SCA-like #Python implementation to get the idea of #SCA compared to #PCA: 👨‍💻 github.com/fabriziomusa... 📚 www.fabriziomusacchio.com/blog/2026-07... #CompNeuro #Neuroscience #NeuralDynamics

Synthetic PCA-vs-SCA-style demonstration. The dataset contains two ground-truth latent processes, mixed single-neuron responses, PCA factors, SCA-style rotated factors, the shared two-dimensional state space, and the L1 objective across possible rotations. The code to reproduce this figure is available in my GitHub repositoryꜛ.

Fabrizio Musacchio@fabmusacchio· 24d

Please find the original paper and #SCA implementation here: 📄 doi.org/10.1016/j.ne... 👨‍💻 github.com/glaserlab/sca #Neuroscience #CompNeuro #NeuralDynamics

Graphical abstract of Zimnik et al. (2026). Sparse component analysis (SCA) is an unsupervised dimensionality reduction method that, unlike PCA, does not only seek a low-dimensional reconstruction of neural population activity, but encourages latent factors to be temporally sparse and therefore more aligned with separable computations. In this post, we walk through the maths and main results behind this idea. Source: Zimnik et al. (2026), Neuron / Cell Press, 10.1016/j.neuron.2026.05.022ꜛ. © 2026 The Authors. Published by Elsevier Inc. Licensed under CC BY-NC-ND 4.0.

Figure 2A-D. Center-out reaching task, behavior, example neurons, and PCA factors. The single-neuron responses and PCA factors mix preparation, execution, posture, and return-related activity. Source: Zimnik et al. (2026), Neuron / Cell Press, 10.1016/j.neuron.2026.05.022ꜛ. © 2026 The Authors. Published by Elsevier Inc. Licensed under CC BY-NC-ND 4.0.

Figure 2E-I. SCA identifies factors primarily active during preparation, execution, or posture. It preserves reconstruction performance relative to weighted PCA while increasing epoch-specific occupancy. Source: Zimnik et al. (2026), Neuron / Cell Press, 10.1016/j.neuron.2026.05.022ꜛ. © 2026 The Authors. Published by Elsevier Inc. Licensed under CC BY-NC-ND 4.0.

Fabrizio Musacchio@fabmusacchio· 25d

@christianpn @mathstodon.xyz 🐘 developed a Chrome browser extension which allows to CTRL+F #maths in PDF. Type eg (\int_0^\infty e^{-x^2},dx) and it highlights every occurrence 👌 🌍 https://chromewebstore.google.com/detail/latex-pdf-search/hljglpckjnkacogbiembidpkllmjkeeh #LaTeX #Mathematics

Fabrizio Musacchio@fabmusacchio· 29d

A recent visit to the #YayoiKusama exhibition at the #MuseumLudwig in #Cologne proved that I’m already very neuro-biased: In many of her paintings, I see nothing but … #dendrites and #spines, #microglia, cell membranes… 🙈😅

Fabrizio Musacchio@fabmusacchio· Jun 22

🧠How does the #hippocampus keep a spatial map stable while adding aversive context? Miguel-López et al show that 🐁 #CA3 doesn’t replace spatial 🗺️ w an aversive one. The spatial #manifold stays stable while an 🌬️ deforms it, embedding affective context into the same geometry: doi.org/10.1073/pnas...

Fabrizio Musacchio@fabmusacchio· Jun 18

… The computation relies on distributed #dendritic nonlinearities, esp. #NMDA: 📄 https://doi.org/10.64898/2026.06.08.730984 🧵2/2 #CompNeuro #Neuroscience 🧪

Fabrizio Musacchio@fabmusacchio· Jun 16

The #NEST Conference 2026 has just started! I'm looking forward to two days of talks and discussions on #NeuralNetworks and the latest advances in the #NESTSimulator ✌️ Btw: We're using Gather Town again and I love creating these #8bit-like avatars there 👾

Fabrizio Musacchio@fabmusacchio· Jun 15

I just pushed #OMIO to version v0.2.2. You can now reuse existing disk-backed #Zarr caches instead of rebuilding them every time an image is opened. OMIO stores cache metadata directly in the Zarr store and validates compatibility automatically before reuse ✌️ 🌍 omio.readthedocs.io/en/latest/us...

Fabrizio Musacchio@fabmusacchio· Jun 12

If you'd like to contribute 🤝, report 🐞, request features 🚀 or new file format support 🗳️, feel free to contact me via #OMIO's GitHub issues: 👨‍💻 github.com/FabrizioMusa... #OpenSource #Python #Microscopy

Fabrizio Musacchio@fabmusacchio· Jun 12

Working with large microscopy collections, e.g., entire experiment series? #OMIO includes #BIDS-like batch conversion workflows ⚙️ that can traverse project trees and convert datasets automatically while applying the same semantic rules to every file. No format-specific batch scripts required. 🧵6/7

Fabrizio Musacchio@fabmusacchio· Jun 12

For large microscopy datasets (e.g. >1 GB): #OMIO can materialize images directly as disk-backed #Zarr stores. This allows #MemoryMapped, slice-wise access w/o loading the entire dataset into RAM. And: It fully integrates with #Napari workflows ✌️ 🧵4/7

Fabrizio Musacchio@fabmusacchio· Jun 12

A major goal of #OMIO is to make image semantics explicit: ✓ normalizes axis order ✓ preserves singleton dimensions ✓ extracts physical scales when available ✓ keeps metadata accessible ✓ warns when critical metadata are missing No more guessing whether the array is TZCYX, ZCYX, CZYX, ... 🧵3/7

Fabrizio Musacchio@fabmusacchio· Jun 12

If you work with #microscopy images 🧫🦠🧠🔬 in #Python 🐍👨‍💻, you may know the situation: Different file formats, readers, axis conventions, metadata structures…At least I found this increasingly frustrating! So I built #OMIO, a unified microscopy image reader & writer: 🌍 omio.readthedocs.io 🧵1/7

Fabrizio Musacchio@fabmusacchio· Jun 4

New paper by Grieves, Duvelle & Taube: Rat #hippocampal #PlaceCells map terrain geometry independently of #behavior. On ridged “hillscape” terrain, #PlaceFields remapped, aligned with terrain contours & repeated across similar #topography: 📄 https://doi.org/10.1126/sciadv.adz9893 #Neuroscience 🧪