Hippocampus @ 1st HBP Platform Release


#1

Dear Hippocampus Colleages,

For those of you who missed it, the Brain Simulation Platform (BSP) Demo
(15mins) can be watched here:


In the first 5 minutes, Felix gives an overview what the objectives of
the Brain Simulation Platform are (what? you mean we can’t solve
everything? :wink: ). In the 2nd 5 minutes, I give an overview of the BSP
applied to the hippocampus.

If you’re interested to take a look around the HBP Collaboratory,
please just let me know, and I can invite you, and also add you to the
Hippocampus Collab. Note, a big issue is still that we’re not able to
give HPC time away for free to anyone off the street. But for the
hippocampus project, there are possibilities to get time on the BBP
BG/Q to help us develop, refine, validate and study the model at this
early draft stage. Please contact me if you’re interested.

Also, several have expressed interest in the automated simplification
pipeline, which I’m happy to report is working surprisingly well, on
the example of the BBP somatosensory cortex model! For more details, and
numbers, there is now a pre-print on arXiv:


A quick screencast describing that is here:


This is an important part of our community building strategy, as it
allows data-integration to happen iteratively on detailed models on the
one hand, from which minimal models for specific hypothesis-driven
studies can be derived in a automated way, and validated against the
data-driven reference. Effectively, this bridges the contentious issue
of what level of detail to choose. Now we can be pluralistic, and
propagate insights back and forth (the simplification is preserving
approximate neuron identity in the circuit! - see the preprint, e.g.
figure 9 compared to the same in the Markram et al, 2015).

Also, for those who missed it, BluePyOpt is our new opensource tool for
optimizing neurons. Here’s a preprint: http://arxiv.org/abs/1603.00500
A quick screencast describing that is here:
https://www.youtube.com/watch?v=I_nz7vNRIrk

Looking forward to your thoughts and feedback.

All the best,
Eilif


#2

That is very cool. Nice to see progress on simplification.


#3

Dear All,

I would like to share these articles (from work at King’s College London - where I’ll be based this September onwards), which just came to my attention only recently as I was working on computational simulations of the hippocampal formation and related areas, and the functional connectome of these hippocampal neural networks. I thought people on this platform might be interested if they haven’t already come across them.

“Voxel-wise comparisons of cellular microstructure and diffusion-MRI in mouse hippocampus using 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND)” by Stolp et al (2018)
https://www.nature.com/articles/s41598-018-22295-9

“Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project” by Bastiani et al (2018)
https://www.sciencedirect.com/science/article/pii/S1053811918304889?via%3Dihub.

“Hippocampal Subfield Volumetry: Differential Pattern of Atrophy in Different Forms of Genetic Frontotemporal Dementia” by Bocchetta et al (2018)
https://content.iospress.com/articles/journal-of-alzheimers-disease/jad180195

“Ammon’s Horn 2 (CA2) of the Hippocampus: A Long-Known Region with a New Potential Role in Neurodegeneration” by Pang et al (2018)
http://journals.sagepub.com/doi/10.1177/1073858418778747

“The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction” by Makropoulos et al (2018)

I’ll share more in the future as I carry out more research in Hippocampal Computational Models at KCL.

Harry M.

Graduate Research, IoPPN, King’s College London (2018-)
Director & Chief Developer, Multidisciplinary Neuroscientific Technologies Ltd (2016-present)
BSc (Neurosciences) University College London (2013-2016)