@maxeggl.bsky.social
Reposted
Huge thanks to:
🔹 David Moratal - @upv.es
🔹 @plopezlarrubia.bsky.social - @iibm-csic-uam.bsky.social
🔹 Mohamed Selim - @uniofnottingham.bsky.social
🔹 From @neuroalc.bsky.social: Santiago Canals @canalslab.bsky.social, Silvia De Santis @desantislab.bsky.social & @maxeggl.bsky.social 🙌
🔹 David Moratal - @upv.es
🔹 @plopezlarrubia.bsky.social - @iibm-csic-uam.bsky.social
🔹 Mohamed Selim - @uniofnottingham.bsky.social
🔹 From @neuroalc.bsky.social: Santiago Canals @canalslab.bsky.social, Silvia De Santis @desantislab.bsky.social & @maxeggl.bsky.social 🙌
July 11, 2025 at 3:26 PM
Huge thanks to:
🔹 David Moratal - @upv.es
🔹 @plopezlarrubia.bsky.social - @iibm-csic-uam.bsky.social
🔹 Mohamed Selim - @uniofnottingham.bsky.social
🔹 From @neuroalc.bsky.social: Santiago Canals @canalslab.bsky.social, Silvia De Santis @desantislab.bsky.social & @maxeggl.bsky.social 🙌
🔹 David Moratal - @upv.es
🔹 @plopezlarrubia.bsky.social - @iibm-csic-uam.bsky.social
🔹 Mohamed Selim - @uniofnottingham.bsky.social
🔹 From @neuroalc.bsky.social: Santiago Canals @canalslab.bsky.social, Silvia De Santis @desantislab.bsky.social & @maxeggl.bsky.social 🙌
However, this time I managed! I would like to thank
@silviadesantis.bsky.social @desantislab.bsky.social for the incredible support, which I think was exactly the difference that allowed me to succeed this year. Now on to more science and research at the intersection between neuroscience and ML!
@silviadesantis.bsky.social @desantislab.bsky.social for the incredible support, which I think was exactly the difference that allowed me to succeed this year. Now on to more science and research at the intersection between neuroscience and ML!
July 1, 2025 at 9:02 AM
However, this time I managed! I would like to thank
@silviadesantis.bsky.social @desantislab.bsky.social for the incredible support, which I think was exactly the difference that allowed me to succeed this year. Now on to more science and research at the intersection between neuroscience and ML!
@silviadesantis.bsky.social @desantislab.bsky.social for the incredible support, which I think was exactly the difference that allowed me to succeed this year. Now on to more science and research at the intersection between neuroscience and ML!
9/
💡 SpyDen bridges the gap between molecular-resolution imaging and user-friendly analysis.
If you’re doing fluorescence imaging of neurons—check it out.
Reproducible, customizable, and made for the community.
#OpenScience #Neuroinformatics #Microscopy
💡 SpyDen bridges the gap between molecular-resolution imaging and user-friendly analysis.
If you’re doing fluorescence imaging of neurons—check it out.
Reproducible, customizable, and made for the community.
#OpenScience #Neuroinformatics #Microscopy
June 20, 2025 at 10:59 AM
9/
💡 SpyDen bridges the gap between molecular-resolution imaging and user-friendly analysis.
If you’re doing fluorescence imaging of neurons—check it out.
Reproducible, customizable, and made for the community.
#OpenScience #Neuroinformatics #Microscopy
💡 SpyDen bridges the gap between molecular-resolution imaging and user-friendly analysis.
If you’re doing fluorescence imaging of neurons—check it out.
Reproducible, customizable, and made for the community.
#OpenScience #Neuroinformatics #Microscopy
8/
📦 Get it here:
Code: github.com/meggl23/SpyDen
Compiled executables: gin.g-node.org/CompNeuroNet...
Documentation & tutorials included. This is an ongoing project so we’d love feedback from the community!
📦 Get it here:
Code: github.com/meggl23/SpyDen
Compiled executables: gin.g-node.org/CompNeuroNet...
Documentation & tutorials included. This is an ongoing project so we’d love feedback from the community!
GitHub - meggl23/SpyDen: The codebase for the SpyDen tool (under preparation)
The codebase for the SpyDen tool (under preparation) - meggl23/SpyDen
github.com
June 20, 2025 at 10:59 AM
8/
📦 Get it here:
Code: github.com/meggl23/SpyDen
Compiled executables: gin.g-node.org/CompNeuroNet...
Documentation & tutorials included. This is an ongoing project so we’d love feedback from the community!
📦 Get it here:
Code: github.com/meggl23/SpyDen
Compiled executables: gin.g-node.org/CompNeuroNet...
Documentation & tutorials included. This is an ongoing project so we’d love feedback from the community!
7/
🖥️ Works out of the box:
• For coders & non-coders
• Trained networks available
• No need to install complex dependencies
• Built for transparency and customization
🖥️ Works out of the box:
• For coders & non-coders
• Trained networks available
• No need to install complex dependencies
• Built for transparency and customization
June 20, 2025 at 10:58 AM
7/
🖥️ Works out of the box:
• For coders & non-coders
• Trained networks available
• No need to install complex dependencies
• Built for transparency and customization
🖥️ Works out of the box:
• For coders & non-coders
• Trained networks available
• No need to install complex dependencies
• Built for transparency and customization
6/
🧪 We validated SpyDen against expert annotations across diverse datasets and use cases.
It performs reliably, making it suitable for both exploratory research and reproducible pipelines.
🧪 We validated SpyDen against expert annotations across diverse datasets and use cases.
It performs reliably, making it suitable for both exploratory research and reproducible pipelines.
June 20, 2025 at 10:58 AM
6/
🧪 We validated SpyDen against expert annotations across diverse datasets and use cases.
It performs reliably, making it suitable for both exploratory research and reproducible pipelines.
🧪 We validated SpyDen against expert annotations across diverse datasets and use cases.
It performs reliably, making it suitable for both exploratory research and reproducible pipelines.
5/
🧰 What can SpyDen do?
• Detect neurites & synapses
• Track fluorescent puncta over time
• Analyze intensity & localization
• Export data in standard formats
• All with a GUI and video tutorials for onboarding
🧰 What can SpyDen do?
• Detect neurites & synapses
• Track fluorescent puncta over time
• Analyze intensity & localization
• Export data in standard formats
• All with a GUI and video tutorials for onboarding
June 20, 2025 at 10:57 AM
5/
🧰 What can SpyDen do?
• Detect neurites & synapses
• Track fluorescent puncta over time
• Analyze intensity & localization
• Export data in standard formats
• All with a GUI and video tutorials for onboarding
🧰 What can SpyDen do?
• Detect neurites & synapses
• Track fluorescent puncta over time
• Analyze intensity & localization
• Export data in standard formats
• All with a GUI and video tutorials for onboarding
4/
✅ Enter SpyDen:
A Python-based platform designed to address this with 3 core goals:
1️⃣ Easy to use for multiple tasks
2️⃣ Fully open-source, with open data formats
3️⃣ Editable annotations, robust across resolutions
✅ Enter SpyDen:
A Python-based platform designed to address this with 3 core goals:
1️⃣ Easy to use for multiple tasks
2️⃣ Fully open-source, with open data formats
3️⃣ Editable annotations, robust across resolutions
June 20, 2025 at 10:57 AM
4/
✅ Enter SpyDen:
A Python-based platform designed to address this with 3 core goals:
1️⃣ Easy to use for multiple tasks
2️⃣ Fully open-source, with open data formats
3️⃣ Editable annotations, robust across resolutions
✅ Enter SpyDen:
A Python-based platform designed to address this with 3 core goals:
1️⃣ Easy to use for multiple tasks
2️⃣ Fully open-source, with open data formats
3️⃣ Editable annotations, robust across resolutions
3/
❌ Most workflows today:
• Multiple software packages
• Custom scripts
• Manual annotation
• Poor reproducibility
• Limited scalability
And many AI tools are not general-purpose, not open, or hard to modify.
❌ Most workflows today:
• Multiple software packages
• Custom scripts
• Manual annotation
• Poor reproducibility
• Limited scalability
And many AI tools are not general-purpose, not open, or hard to modify.
June 20, 2025 at 10:57 AM
3/
❌ Most workflows today:
• Multiple software packages
• Custom scripts
• Manual annotation
• Poor reproducibility
• Limited scalability
And many AI tools are not general-purpose, not open, or hard to modify.
❌ Most workflows today:
• Multiple software packages
• Custom scripts
• Manual annotation
• Poor reproducibility
• Limited scalability
And many AI tools are not general-purpose, not open, or hard to modify.
2/
🔍 Motivation:
Studying learning and memory means understanding molecules inside axons, dendrites, and synapses.
Modern microscopy can detect single molecules—
…but analyzing those images? Still often manual, fragmented, or semi-automated.
🔍 Motivation:
Studying learning and memory means understanding molecules inside axons, dendrites, and synapses.
Modern microscopy can detect single molecules—
…but analyzing those images? Still often manual, fragmented, or semi-automated.
June 20, 2025 at 10:57 AM
2/
🔍 Motivation:
Studying learning and memory means understanding molecules inside axons, dendrites, and synapses.
Modern microscopy can detect single molecules—
…but analyzing those images? Still often manual, fragmented, or semi-automated.
🔍 Motivation:
Studying learning and memory means understanding molecules inside axons, dendrites, and synapses.
Modern microscopy can detect single molecules—
…but analyzing those images? Still often manual, fragmented, or semi-automated.
Our pop science article (in Spanish 🇪🇸) breaks it down for everyone: shorturl.at/esXTu
And check out the preprint too: shorturl.at/8agYv
@neuroalc.bsky.social
🧵
And check out the preprint too: shorturl.at/8agYv
@neuroalc.bsky.social
🧵
Menos tiempo, mejor diagnóstico: cuando la IA alivia las listas de espera en resonancia magnética
La IA permite reducir drásticamente el tiempo de exploración en resonancias magnéticas, aliviando listas de espera en hospitales. ¿La clave? Utilizar datos simulados en su entrenamiento para obtener i...
shorturl.at
April 30, 2025 at 12:54 PM
Our pop science article (in Spanish 🇪🇸) breaks it down for everyone: shorturl.at/esXTu
And check out the preprint too: shorturl.at/8agYv
@neuroalc.bsky.social
🧵
And check out the preprint too: shorturl.at/8agYv
@neuroalc.bsky.social
🧵
Why this matters:
✔️ Shorter, more comfortable scans
✔️ More patients can get high-quality imaging
✔️ Older, noisy datasets can now be rescued
✔️ Clinics can finally use advanced dw-MRI tools
All without needing to share or store sensitive patient data. (6/n)
✔️ Shorter, more comfortable scans
✔️ More patients can get high-quality imaging
✔️ Older, noisy datasets can now be rescued
✔️ Clinics can finally use advanced dw-MRI tools
All without needing to share or store sensitive patient data. (6/n)
April 30, 2025 at 12:53 PM
Why this matters:
✔️ Shorter, more comfortable scans
✔️ More patients can get high-quality imaging
✔️ Older, noisy datasets can now be rescued
✔️ Clinics can finally use advanced dw-MRI tools
All without needing to share or store sensitive patient data. (6/n)
✔️ Shorter, more comfortable scans
✔️ More patients can get high-quality imaging
✔️ Older, noisy datasets can now be rescued
✔️ Clinics can finally use advanced dw-MRI tools
All without needing to share or store sensitive patient data. (6/n)
We trained SBI to estimate key diffusion parameters from fewer MRI measurements — and it worked.
✨ 90% faster scans
✨ High accuracy preserved
✨ Robust even with noisy data
(5/n)
✨ 90% faster scans
✨ High accuracy preserved
✨ Robust even with noisy data
(5/n)
April 30, 2025 at 12:53 PM
We trained SBI to estimate key diffusion parameters from fewer MRI measurements — and it worked.
✨ 90% faster scans
✨ High accuracy preserved
✨ Robust even with noisy data
(5/n)
✨ 90% faster scans
✨ High accuracy preserved
✨ Robust even with noisy data
(5/n)
Enter: Simulation-Based Inference (SBI) — a new AI approach that flips the script.
Instead of training on huge amounts of real patient data, SBI learns from simulated data and can handle noisy, sparse measurements much more efficiently. (4/n)
Instead of training on huge amounts of real patient data, SBI learns from simulated data and can handle noisy, sparse measurements much more efficiently. (4/n)
April 30, 2025 at 12:53 PM
Enter: Simulation-Based Inference (SBI) — a new AI approach that flips the script.
Instead of training on huge amounts of real patient data, SBI learns from simulated data and can handle noisy, sparse measurements much more efficiently. (4/n)
Instead of training on huge amounts of real patient data, SBI learns from simulated data and can handle noisy, sparse measurements much more efficiently. (4/n)
Current methods need to oversample like crazy to get good-quality maps. That’s why advanced diffusion imaging is rarely used outside high-end research labs.
Patients? They get the basics—if they’re lucky. (3/n)
Patients? They get the basics—if they’re lucky. (3/n)
April 30, 2025 at 12:53 PM
Current methods need to oversample like crazy to get good-quality maps. That’s why advanced diffusion imaging is rarely used outside high-end research labs.
Patients? They get the basics—if they’re lucky. (3/n)
Patients? They get the basics—if they’re lucky. (3/n)
Diffusion-weighted MRI (dw-MRI) is a powerhouse in neuroimaging — revealing microstructural details of the brain without invasive procedures.
But there’s a catch: it’s slow and resource-heavy. Long scans = longer waitlists + fewer patients helped. (2/n)
But there’s a catch: it’s slow and resource-heavy. Long scans = longer waitlists + fewer patients helped. (2/n)
April 30, 2025 at 12:53 PM
Diffusion-weighted MRI (dw-MRI) is a powerhouse in neuroimaging — revealing microstructural details of the brain without invasive procedures.
But there’s a catch: it’s slow and resource-heavy. Long scans = longer waitlists + fewer patients helped. (2/n)
But there’s a catch: it’s slow and resource-heavy. Long scans = longer waitlists + fewer patients helped. (2/n)
Incredible discussions and insights—already excited for next year’s edition! Interested in joining or learning more? Follow us for future updates, and stay tuned! 🚀 #Workshop #Neuroscience #AI
April 28, 2025 at 8:26 AM
Incredible discussions and insights—already excited for next year’s edition! Interested in joining or learning more? Follow us for future updates, and stay tuned! 🚀 #Workshop #Neuroscience #AI
16 talented participants explored exciting frontiers at the intersection of neuroscience and AI. This year’s focus: dimensionality reduction and understanding high-dimensional data through dynamical systems. #DimensionalityReduction #DataScience
April 28, 2025 at 8:26 AM
16 talented participants explored exciting frontiers at the intersection of neuroscience and AI. This year’s focus: dimensionality reduction and understanding high-dimensional data through dynamical systems. #DimensionalityReduction #DataScience
Don't miss out on this opportunity! Link to the application (deadline 21st of February): shorturl.at/s9RNI (flyer with more information here: rb.gy/21z6l9)
Application Bio-inspired deep-learning workshop
Application form for the Bio-inspired deep learning Workshop at the Weingut Domhof in Guntersblum (close to Mainz) from the 22nd to the 25th of April. Led by Dr. Angus Chadwick, it will provide hands-...
shorturl.at
January 31, 2025 at 5:21 PM
Don't miss out on this opportunity! Link to the application (deadline 21st of February): shorturl.at/s9RNI (flyer with more information here: rb.gy/21z6l9)