---
_id: '21971'
abstract:
- lang: eng
text: "A Rust library for analyzing dendritic structures using quadric matrices.
This project provides efficient tools for representing dendritic trees, computing
quadric error metrics, and visualizing eigenvalue distributions on hexagonal plots.\r\n\r\nThis
library implements quadric-based geometric analysis of dendritic structures, commonly
found in neuroscience applications. Key features include:\r\n\r\nTree data structures:
Hierarchical vertex and edge representations for dendritic trees\r\nQuadric matrices:
Computation of quadric error metrics for edges and vertices\r\nVisualisation:
Hexagonal plot generation using NormPolar transformations\r\nInteractive tools:
Desktop application with plotting capabilities"
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
- first_name: Emanuele
full_name: Cortinovis, Emanuele
last_name: Cortinovis
citation:
ama: Bokor Bleile Y, Cortinovis E. Quadrix. 2026. doi:10.15479/AT-ISTA-21971
apa: Bokor Bleile, Y., & Cortinovis, E. (2026). Quadrix. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-21971
chicago: Bokor Bleile, Yossi, and Emanuele Cortinovis. “Quadrix.” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21971.
ieee: Y. Bokor Bleile and E. Cortinovis, “Quadrix.” Institute of Science and Technology
Austria, 2026.
ista: Bokor Bleile Y, Cortinovis E. 2026. Quadrix, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21971.
mla: Bokor Bleile, Yossi, and Emanuele Cortinovis. Quadrix. Institute of
Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21971.
short: Y. Bokor Bleile, E. Cortinovis, (2026).
corr_author: '1'
date_created: 2026-06-09T19:19:13Z
date_published: 2026-06-15T00:00:00Z
date_updated: 2026-06-15T23:00:03Z
day: '15'
department:
- _id: HeEd
doi: 10.15479/AT-ISTA-21971
file:
- access_level: open_access
checksum: 48f633b6767c4b15dd6220ca2b4dc175
content_type: application/octet-stream
creator: ybleile
date_created: 2026-06-09T19:16:02Z
date_updated: 2026-06-09T19:16:02Z
file_id: '21974'
file_name: LICENSE
file_size: 1081
relation: main_file
success: 1
- access_level: open_access
checksum: de25d0b224acbde3d38f837fdd8f97d5
content_type: application/octet-stream
creator: ybleile
date_created: 2026-06-09T19:16:27Z
date_updated: 2026-06-09T19:16:27Z
file_id: '21975'
file_name: quadrix-x64.exe
file_size: 11308032
relation: main_file
success: 1
- access_level: open_access
checksum: a7b94a7380dc178e76ebdba9f1fa45c2
content_type: application/octet-stream
creator: ybleile
date_created: 2026-06-09T19:16:28Z
date_updated: 2026-06-09T19:16:28Z
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file_size: 10655744
relation: main_file
success: 1
- access_level: open_access
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content_type: application/zip
creator: ybleile
date_created: 2026-06-09T19:16:27Z
date_updated: 2026-06-09T19:16:27Z
file_id: '21977'
file_name: Quadrix Desktop.app.zip
file_size: 2032
relation: main_file
success: 1
- access_level: open_access
checksum: 106930f81563c5c719a5f4030b5ca5ed
content_type: application/octet-stream
creator: ybleile
date_created: 2026-06-09T19:16:40Z
date_updated: 2026-06-09T19:16:40Z
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file_name: quadrix-arm64
file_size: 12187896
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checksum: 0e6ba129318446676f220087e7e6ff41
content_type: application/octet-stream
creator: ybleile
date_created: 2026-06-09T19:16:52Z
date_updated: 2026-06-09T19:16:52Z
file_id: '21979'
file_name: quadrix-x64
file_size: 20587592
relation: main_file
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- access_level: open_access
checksum: f0b03385d17df049219465ab7403fe09
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2026-06-09T19:19:12Z
date_updated: 2026-06-09T19:19:12Z
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file_name: Quadrix.zip
file_size: 1914198
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checksum: ede0bbb24bf41ab4009cf1b6a9009671
content_type: application/zip
creator: ybleile
date_created: 2026-06-10T19:09:38Z
date_updated: 2026-06-10T19:09:38Z
file_id: '21993'
file_name: THIRD_PARTY_LICENSES.zip
file_size: 37557
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- access_level: open_access
checksum: f3c5fcc62c88e449ab5c660244df5aef
content_type: text/markdown
creator: ybleile
date_created: 2026-06-15T08:13:32Z
date_updated: 2026-06-15T08:13:32Z
file_id: '22009'
file_name: README.md
file_size: 3839
relation: main_file
success: 1
- access_level: open_access
checksum: aa74828c3165aafcdee4ddcc9ecd37ac
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2026-06-15T08:14:24Z
date_updated: 2026-06-15T08:14:24Z
file_id: '22008'
file_name: Quadrix.zip
file_size: 1912923
relation: main_file
file_date_updated: 2026-06-15T08:14:24Z
fulldoi: https://doi.org/10.15479/AT-ISTA-21971
has_accepted_license: '1'
keyword:
- quadratics
- mathematics
- dendrites
- geometry
- topology
license: https://opensource.org/licenses/MIT
month: '06'
oa: 1
project:
- _id: 9106a876-16d5-11f0-9cad-bbf11c9952f9
grant_number: ESP 9584724
name: Quantitative Unbiased Shape Analysis with Geometry & Topology
publisher: Institute of Science and Technology Austria
status: public
title: Quadrix
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
_id: '21442'
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
citation:
ama: Schlögl A. CA3Simu v1.06 (vargas2026v1). 2026. doi:10.15479/AT-ISTA-21442
apa: Schlögl, A. (2026). CA3Simu v1.06 (vargas2026v1). Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-21442
chicago: Schlögl, Alois. “CA3Simu v1.06 (Vargas2026v1).” Institute of Science and
Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21442.
ieee: A. Schlögl, “CA3Simu v1.06 (vargas2026v1).” Institute of Science and Technology
Austria, 2026.
ista: Schlögl A. 2026. CA3Simu v1.06 (vargas2026v1), Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21442.
mla: Schlögl, Alois. CA3Simu v1.06 (Vargas2026v1). Institute of Science and
Technology Austria, 2026, doi:10.15479/AT-ISTA-21442.
short: A. Schlögl, (2026).
corr_author: '1'
date_created: 2026-03-12T08:20:46Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-07-01T06:47:49Z
day: '12'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.15479/AT-ISTA-21442
ec_funded: 1
file:
- access_level: open_access
checksum: 441c8827717dcda05f91c127d15cf1e9
content_type: application/gzip
creator: schloegl
date_created: 2026-03-12T08:19:14Z
date_updated: 2026-03-12T08:19:14Z
file_id: '21443'
file_name: ca3simu-vargas2026v1.tar.gz
file_size: 160410
relation: main_file
success: 1
- access_level: open_access
checksum: 3c0092076228a15c0a7ae703192d43ea
content_type: text/markdown
creator: schloegl
date_created: 2026-03-12T10:24:45Z
date_updated: 2026-03-12T10:24:45Z
file_id: '21445'
file_name: README.md
file_size: 10923
relation: main_file
success: 1
file_date_updated: 2026-03-12T10:24:45Z
fulldoi: https://doi.org/10.15479/AT-ISTA-21442
has_accepted_license: '1'
keyword:
- hypocampus
- ca3 simulations
- modelling
license: https://opensource.org/licenses/GPL-3.0
month: '03'
oa: 1
project:
- _id: e62b56fe-ab3c-11f0-94c7-d181dd352b3b
grant_number: '101199096'
name: Synaptic mechanisms of engram storage and retrieval in CA3 hippocampal microcircuits
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e
grant_number: PAT 4178023
name: Synaptic networks of human brain
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '22229'
relation: used_in_publication
status: public
status: public
title: CA3Simu v1.06 (vargas2026v1)
tmp:
legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html
name: GNU General Public License 3.0
short: GPL 3.0
type: software
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
_id: '14926'
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926
apa: Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14926
chicago: Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14926.
ieee: R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of
Science and Technology Austria, 2024.
ista: Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:14926.
mla: Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. Institute
of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14926.
short: R. Hauschild, (2024).
corr_author: '1'
date_created: 2024-02-02T14:42:26Z
date_published: 2024-02-02T00:00:00Z
date_updated: 2026-10-01T08:32:33Z
day: '02'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:14926
file:
- access_level: open_access
checksum: df7f358ae19a176cf710c0a802ce31b1
content_type: application/octet-stream
creator: rhauschild
date_created: 2024-02-02T14:40:31Z
date_updated: 2024-02-02T14:40:31Z
file_id: '14927'
file_name: README.md
file_size: 736
relation: main_file
success: 1
- access_level: open_access
checksum: 10194cc11619eccd8f4b24472e465b7f
content_type: application/x-zip-compressed
creator: rhauschild
date_created: 2024-02-02T14:40:31Z
date_updated: 2024-02-02T14:40:31Z
file_id: '14928'
file_name: Supplementary_file_1.zip
file_size: 3543
relation: main_file
success: 1
file_date_updated: 2024-02-02T14:40:31Z
fulldoi: https://doi.org/10.15479/AT:ISTA:14926
has_accepted_license: '1'
month: '02'
oa: 1
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '15048'
relation: used_in_publication
status: public
status: public
title: Matlab script for analysis of clone dispersal
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14502'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized fila- mentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023.
doi:10.15479/AT:ISTA:14502
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:14502.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data.” Institute of Science and Technology Austria, 2023.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.
mla: Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14502.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).
corr_author: '1'
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2026-07-06T12:57:43Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
file:
- access_level: open_access
checksum: a8b9adeb53a4109dea4d5e39fa1acccf
content_type: application/zip
creator: fschur
date_created: 2023-11-08T20:23:07Z
date_updated: 2023-11-08T20:23:07Z
file_id: '14503'
file_name: Computational_Toolbox_v1.2.zip
file_size: 347641117
relation: main_file
success: 1
- access_level: open_access
checksum: 14db2addbfca61a085ba301ed6f2900b
content_type: text/plain
creator: dernst
date_created: 2023-11-21T08:20:23Z
date_updated: 2023-11-21T08:20:23Z
file_id: '14586'
file_name: Readme.txt
file_size: 1522
relation: main_file
success: 1
file_date_updated: 2023-11-21T08:20:23Z
fulldoi: https://doi.org/10.15479/AT:ISTA:14502
has_accepted_license: '1'
keyword:
- cryo-electron tomography
- actin cytoskeleton
- toolbox
license: https://choosealicense.com/licenses/agpl-3.0/
month: '11'
oa: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10290'
relation: used_for_analysis_in
status: public
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
tmp:
legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html
name: GNU Affero General Public License v3.0
short: 'GNU AGPLv3 '
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '9327'
abstract:
- lang: eng
text: "This archive contains the missing sweater mesh animations and displacement
models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode
Repository: https://git.ist.ac.at/gsperl/MADYPG"
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.
https://doi.org/10.15479/AT:ISTA:9327.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data).” IST Austria, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.
mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.
short: G. Sperl, R. Narain, C. Wojtan, (2021).
date_created: 2021-04-16T14:26:19Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2026-06-18T19:57:47Z
ddc:
- '005'
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/AT:ISTA:9327
file:
- access_level: open_access
checksum: 0324cb519273371708743f3282e7c081
content_type: application/zip
creator: gsperl
date_created: 2021-04-16T14:15:12Z
date_updated: 2021-04-16T14:15:12Z
file_id: '9328'
file_name: MADYPG_extra_data.zip
file_size: 802586232
relation: main_file
success: 1
- access_level: open_access
checksum: 4c224551adf852b136ec21a4e13f0c1b
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2021-04-26T09:33:44Z
date_updated: 2021-04-26T09:33:44Z
file_id: '9353'
file_name: MADYPG.zip
file_size: 64962865
relation: main_file
file_date_updated: 2021-04-26T09:33:44Z
fulldoi: https://doi.org/10.15479/AT:ISTA:9327
gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573
gitlab_url: https://git.ist.ac.at/gsperl/MADYPG
has_accepted_license: '1'
month: '05'
oa: 1
publisher: IST Austria
related_material:
record:
- id: '9818'
relation: used_for_analysis_in
status: public
status: public
title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model
Data)
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
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Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
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ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
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