====== bam33nin -- Neuroinformatika / Neuroinformatics ====== ====== Výuka | Course info ====== /* **Online výuka (přednášky) probíhají dle rozvrhu na tomto odkazu [[https://meet.google.com/ehc-shyf-aic|https://meet.google.com/ehc-shyf-aic]] ** */ [[https://cw.fel.cvut.cz/b192/courses/bam33nin/podminky|Podmínky předmětu a způsob hodnocení/ Course conditions and evaluation method]] [[https://intranet.fel.cvut.cz/cz/education/rozvrhy-ng.B232/public/html/predmety/54/67/p5467506.html| Rozvrh BAM33NIN 2023/2024]] [[https://intranet.fel.cvut.cz/cz/education/rozvrhy-ng.B232/public/html/predmety/55/01/p5501406.html| Schedule BEAM33NIN 2023/2024]] The course will be taught in a hybrid format: CTU students will attend in person, while international students will be invited to join via Zoom. Please note that all lectures and lab exercises will be recorded. The course sessions are scheduled for every Wednesday at 12:45 PM CET/CEST ([[https://feectu.zoom.us/j/96578509841|ZOOM link lectures]]), with laboratory sessions commencing at 4:15 PM CET/CEST([[https://feectu.zoom.us/j/92565944239|ZOOM link labs]]). Throughout the course, we will explore the fundamentals of information processing at the neural single/muliti-cell level. It is also my honour to have esteemed colleagues join us as guest speakers, who are experts in computational neuroscience. **David Kala** will discuss brain vascularization, an often overlooked yet critical topic. Neuroscientist and clinician **Pavel Filip** will share insights on advanced techniques in deep brain stimulation. **Jan Antolik** will delve into the intricacies of visual prosthetics. **Jirka Hammer** will guide us through the world of cognitive neuron processing in the cortex. Lastly, **Karla Stepanova** will address the topic of cognitive modelling, which has significant applications in communication with robots. The internal material can be downloaded here:[[ https://drive.google.com/drive/folders/1PNLpxdJQ_mnAmKDporG4VncyHKdVnE-8?usp=sharing|here]] /* ====== Zkouška | Exam ====== /*The first date will be on Wednesday 7.6.2023 from 13:00-15.00h. The next date is Wednesday 21.6.2023 from 14.00-16.00. The room is my office G202, we will eventually move to G205. The oral exam will last 30 minutes, will consist of 3 questions, one question for about 10 minutes, total 40 points (Q1:13 points,Q2:13 points, Q3:14 points). List of exam topics: {{ :courses:bam33nin:exam_neuroinformatics_2023_en.pdf |}}. Zkouška proběhne distanční formou na tomto odkazu: [[https://meet.google.com/ehc-shyf-aic|Ústní zkouška]]. */ ====== Přednášky | Lectures ====== - 21.2: Úvod do neuroinformatiky, organizace předmětu, model membrány | //Introduction// {{{{:courses:beam33nin:lec1-2024.pdf|Lecture 1}}, [[https://drive.google.com/file/d/1Xf_MtRilcJsP4mf9j8WJNqaGa11F4603/view?usp=drive_link|recorded lecture 2024]] - 28.2.: Modely neuronů: iontové kanály, synapse, Hodgkin-Huxley, Wilsonův model | //Neuron models// {{:courses:beam33nin:lec2-2024.pdf|Lecture 2}}, [[ https://drive.google.com/file/d/1ssuM1uZ-Ad7Xij0sVNcukRmmCBETHlYO/view?usp=sharing|recorded lecture 2024]] - 6.3: Hodgkin-Huxley model {{:courses:beam33nin:lec3-2024.pdf|Lecture 3}} , [[https://drive.google.com/file/d/1hyN0oQWu8bU3sR7mwd0U8Ff-PQIa_nIL/view?usp=drive_link|recorded lecture 2024 ]] - 13.3: Případová studie - Parkinsonova nemoc | //Case study: Parkinson's disease// ([[http://bakstein.net|Eduard Bakštein]]){{ :courses:beam33nin:slidesparkinson2024.pdf |Lecture 4}}, [[https://drive.google.com/file/d/1B36IlCsdBTKZSz263iJznzURoRW5qMu8/view?usp=drive_link|Recorded lecture 2024]] - 20.3: Případová studie - Epilepsie a Výzkum mozku pomocí MRI | //Case study - Epillepsy and MRI for Brain research// (David Kala) {{ :courses:beam33nin:nin2024-lec5-davidkala_advancedbrainmri.pdf |Lecture 5}},[[https://drive.google.com/file/d/1OwC2uk0fJj3g7ihfGOWwNm8OdrCHhToR/view|recorded lecture 2024]] - 27.3.: Cable theory, Simplified neuron {{:courses:beam33nin:lec6-2024.pdf|Lecture 6}}, [[https://drive.google.com/file/d/1Savlrk523iBZ16D2lgTlxGoNmM7651hV/view?usp=drive_link|recorded lecture 2024]] - 3.4: Synaptická plasticita | //Synaptic plasticity// {{:courses:beam33nin:lec7-2024.pdf|Lecture 7}}, [[https://drive.google.com/file/d/1fmZGdgiwB8asnKD3J_OA3HJNVoi4Si0S/view?usp=sharing|recorded lecture 2024]] - 10.4: Random networks ex vivo {{:courses:beam33nin:lec8-2024.pdf|Lecture 8}},[[https://drive.google.com/file/d/1kY_D8tkTp6NmqHiZJzZLtEmiQROtMolD/view?usp=sharing|recorded lecture 2024]] - 17.4: Self organizing maps and dynamic neural fields {{:courses:beam33nin:lec9-2024.pdf|Lecture 9}},[[https://drive.google.com/file/d/1SaMJoAv-RzET5LBMn8dZ49rZ6asreBKo/view?usp=sharing, |recorded lecture 2024]] - 24.4: Advanced analysis of MRI signals: Connectomics ([[https://www.researchgate.net/profile/Pavel-Filip|Pavel Filip]]) {{:courses:beam33nin:lec10-2024.pdf|Lecture 10}},[[https://drive.google.com/file/d/109lA-kVdN6g53IgXdLMgf-stSHIO_1y7/view?usp=sharing,|recorded lecture 2024]] - 1.5. svátek - 9.5:(čtvrtek, náhrada výuky) Modelovani vizualniho kortexu|Visual cortex modelling ([[http://antolik.net|Jan Antolik]]) {{:courses:bam33nin:cvut_talk.pdf|Lecture 10}} , [[https://drive.google.com/file/d/1Pj0vzTi_XeeEUiMMtwW1EV2vMa0FmDti/view|recorded lecture]], [[https://drive.google.com/file/d/1k21BHhTrHlyWAp_20z6EX2h1gNEyNpgW/view|discussion]] - 15.5: Rozhraní mozek-počítač | //Brain-computer interfaces // ([[https://www.researchgate.net/profile/Jiri-Hammer-3|Jiří Hammer]]) - 22.5: Kognitivní modelování | //Cognitive modelling// ([[http://karlastepanova.cz(|Karla Štěpánová]]) /*{{:{{:courses:a6m33nin:lectures:pres_test.pdf|Přednáška 14}} */ [[ https://drive.google.com/open?id=1oZrEiTlaiAI4pPJUCCN4WifDy5tg6SmE|recorded lecture]], [[https://drive.google.com/file/d/1yUI8IHXT3sexwfMecfyYZAM9yy7Ozs3z/view|discussion ]] /* - 10.4: Random networks ex vivo {{:courses:bam33nin:lec7.pdf|Lecture 8}},[[https://drive.google.com/file/d/1mIZpaoj7QRVQOsZbrzbjcCzYlJEf6EkV/view|recorded lecture 2021]], [[https://drive.google.com/file/d/1LuAWPgDfbrv5Qu8LTgSAsDIOp4NRfd9T/view|recorded lecture 2020]] - self organizing maps {{:courses:bam33nin:lec12.pdf?nocache|Přednáška 12}}, recorded lecture: https://drive.google.com/file/d/1xLI4x1VwlcCXDMJ9xQmd2QdD3c-cF5hI/view, recorder lecture 2021: https://drive.google.com/open?id=1vs7kHA2C5gJ_i5Ff2ybVy0RHsJqvJBVJ Náhrada výuky /* Kódování, dekódování informace | //Information coding// {{:courses:bam33nin:lec13.pdf?nocache|Přednáška 13}}, [[https://drive.google.com/file/d/1kjkxr-FDgJ9sJH3nXmVG9Caj5WUe83LU/view|recorded lecture]] /* - 3.4: Cortex modelling | //Cortex// {{:courses:bam33nin:lec7.pdf|Přednáška 7}}, [[https://drive.google.com/file/d/1XJ0ZkMT_tnB4UkBsKkUpe-h_vWcqIs8h/view|recorded lecture 2021]],[[https://drive.google.com/file/d/1NMCeWr1axbaaeKcssMEwMtOmgtzpXwAy/view|recorded lecture 2020]] */ /* - 24.4: Vědomí, pozornost, emoce, paměť | Consciousness, attention, emotions, memory ([[https://kognice.wixsite.com/vavrecka|Michal Vavrecka]]) {{:courses:bam33nin:lec10michal.pdf?nocache|Přednáška 10}} [[https://drive.google.com/file/d/1nkjRPPypYTbRKi-YgyTa5HMUKvtag8-W/view| rec lecture I]] , [[https://drive.google.com/file/d/1sPZtBSjvMv0yvfcJDOUtEt0hiO3Q0qWD/view|rec lecture II]] - 31.5: Případová studie: epilepsie | //Case study:epilepsy// (tbd: Jiří Hammer) {{ :courses:bam33nin:lectures:klement.pdf |BONUS od Dana Klementa: Prostorová navigace u zvířat}} Materiály k přednáškám lze stáhnout [[https://147.32.84.236/teach/nin/doc/|zde]]. Přihlašovací údaje byly sděleny na přednáškách. - 25.3: Prostorová navigace u zvířat | //Spatial orientation in animals// (Daniel Klement) {{:courses:a6m33nin:lectures:klement.pdf ?nocache|Přednáška 6}}*/ ====== Cvičení | Lab exercises ====== **{{:courses:beam33nin:a6m33ninlabs2024en.pdf |Instruction for lab exercises}}** (update 9.4.2024) ZOOM link (for international students): https://feectu.zoom.us/j/92565944239 **System for assignment hand-in: https://cw.felk.cvut.cz/brute/** **Labs: in person, room KN:E230** /* ** Google meet link labs: https://meet.google.com/oyg-xukw-nnm (NEW as of 10.3.2021)** */ **Assignments:** All assignments are to be submitted through the BRUTE system (link above). Upload your assignment as a zip archive with all necessary codes with a short pdf report, briefly summarizing the task and showing the results of the simulations. **Deadlines and penalties:** 1 week for completion at full grade, two weeks 50% penalty, 2+ weeks 100% penalty (0 points). All exercises have to be completed and handed in in order to obtain assessment. **Doporučená literatura / //Recommended literature// ** Available from the dept. of Cybernetics' library - contact Dr Petr Novak (novakpe@fel.cvut.cz) [1] Thomas Trappenberg. Fundamentals of Computational Neuroscience. Oxford University Press, USA, June 2010. [2] David Fitzpatrick William C. Hall Anthony-Samuel LaMantia Leonard E. White Dale Purves, George J. Augustine. Neuroscience. Sinauer Associates, Inc., 5th. edition edition, 2011. [3] Michael L. Hines Nicholas T. Carnevale. The Neuron Book. Cambridge University Press, 2006. [4] Werner M. Kistler Wulfram Gerstner. Spiking Neuron Models: Single Neurons, Populations, Plas- ticity. Cambridge University Press, 2002. /* //Lab materials are published continuously during the semester in the list below. The PDF instructions will be continuously updated as well (remember to refresh the pdf page - F5!)// Materiály ke cvičením budou průběžně zveřejňovány v seznamu cvičení, stejnětak PDF instrukce budou průběžně doplňovány (pokud zobrazujete stránku s pdf v prohlížeči, nezapomeňte ji obnovit - F5). [[courses:a3b33kui:plagiaty|Co je a není plagiát?]] */ =====Program cvičení | Exercise materials===== - ** Numerical integration - Euler's method | //Matematický aparát: numerické metody řešení dif. rovnic// ** * 21.2.2024 * //Assignment: Exercise 0.1// * [[https://drive.google.com/file/d/18-zx62y6aBHc7_BLfrrVLveFpwEXu0Vc/view|Ex 0.1 - numerical integration video tutorial (EN)]] (25 min) /*[[https://drive.google.com/file/d/16iQlUNcleLZ6bRWZ83BNUpZtrieGGWJ5/view|Záznam CV1 LS 2021]]*/ * [[https://drive.google.com/file/d/1Udx9uHok4kDrXLbVJmGNhYLB4rk7g-BT/view?usp=drive_link|Recorded LAB 01/2024]] (unfortunately, the first part was not recorded due to connection problems) * {{ :courses:beam33nin:cv0_matlab_introen.m |matlab_intro.m}} (EN, fixed 22.02.2024) * + bezpečnost práce /* * {{:courses:a6m33nin:cv:cv1_numint_base.m| zakladni reseni v matlabu}} (//basic solution in matlab//) */ - ** Neuron models: RC model| //RC model// ** * 28.2.2024 * //Assignment: Exercise 1.1//https://cw.fel.cvut.cz/wiki/lib/images/wrap.gif * [[https://drive.google.com/file/d/1lxg8DOz-MG6pnTnau9_R5mnkMtnbNzg6/view|Ex 1.1 - RC video tutorial (EN)]] (22 min) /*,[[https://drive.google.com/file/d/1cFAgcV6gIgOid7iV0pKtVAQA8vOwxs0I/view | Záznam CV2 LS 2021]] */ - ** EPSP model | //EPSP model// ** * 6.3.2024 * We will discuss the solutions of the first two assignments and work on the EPSP model * //Assignment: No asignment// * [[https://drive.google.com/file/d/1UfqXKxd1Aeo7RXXEh6KO3L0ISnsOSJgX/view|Ex. 1.2 - EPSP video tutorial (EN)]] (23 min) * [[https://drive.google.com/file/d/1btiJERbZZiTQvBrV9wCw62USHEpie3hr/view?usp=drive_link|Recorded LAB 03/2024]] /* * [[https://drive.google.com/file/d/1QuFoD4mxDig27rX45cjuVMeCqEpjYs4e/view?usp=sharing |Záznam CV3 LS 2021]] */ * {{:courses:a6m33nin:tutorials:cv2_2_epsp.m|cv2_epsp.m}} - ** Hodgkin-Huxley model | //Modelování neuronů II - Hodgkin-Huxley // ** * 13.3.2024 * //Assignment: Exercise 1.3// * [[https://drive.google.com/file/d/1cIWyYmAzt0xLn2FFe-9DxLEXZ-m-oCFq/view?usp=sharing| Ex. 1.3 - Hodgkin Huxley video tutorial (EN)]] (36 min) * [[https://drive.google.com/file/d/1vQrtq-dEBI0iod3UeTgoVvM6Y9Em-9R9/view?usp=drive_link|Recorded LAB 04/2024]] /* [[https://drive.google.com/file/d/1147YdB3yBGWsjkbAs_2X0YnNKchWiJUP/view|Záznam CV4 LS 2021]] */ * {{ :courses:a6m33nin:tutorials:cv3_hh.m |cv3_hh.m}} - ** Poisson spiketrain | //Poissonovský spiketrain (+ LIF model)// ** * 20.3.2024 * //Assignment: Exercise 1.4// * [[https://drive.google.com/file/d/1Rv4-YiN3GVjXrIbSH25-AOmUihQITGoL/view|Ex. 1.4 - LIF video tutorial]] (31 min) * {{ :courses:a6m33nin:tutorials:cv4_lif.m |cv4_lif.m}} * [[https://drive.google.com/file/d/15jpFM6zFgAYUoHTkRuO4TILlkGTL3lIE/view?usp=drive_link| Recorded lab 05/2024]] - ** Generation of artificial uEEG, LIF model | //Vytváření simulovaného uEEG signálu, LIF model //** * 27.3.2024 * //Assignment: Exercise 2.1 // * [[https://drive.google.com/file/d/1_hYLC3Byyho68jFJXVI03UQ7hXOqRELO/view|Video tutorial Ex. 2.1]] (21 min) [[https://drive.google.com/file/d/1glrAcqjgsZlnJVjvzE8Z_d0xapSOoq9U/view| Extra tutorial note: matrix reshaping in matlab and common errors]] (18 min) * [[https://drive.google.com/file/d/1s0-Txxd8R1FOXLL7P1mIv7s5rq14JgKf/view?usp=drive_link|Recorded lab 06/2024]] - ** Comparison of real and simulated data | //Porovnání simulovaných dat s reálnými s reálnými//** * 3.4.2024 * //Assignment: Exercise 2.2// * [[https://drive.google.com/file/d/11CnR34nIAzry3zxf1SfsVJgyp74r9WOY/view|Ex. 2.2 - video tutorial]] (35 min), * Spike templates: {{ :courses:a6m33nin:tutorials:cv6_spikeset.mat |cv6_spikeset.mat}} * Real micro-EEG data: {{ :courses:a6m33nin:tutorials:cv6_realmeeg.mat |cv6_realmeeg.mat}} (fs=24kHz) * [[https://drive.google.com/file/d/1Hi8p5xYI6HLcNf7UsQyqYtj0ffotWv9-/view?usp=drive_link|Recorded lab 07/2024]] /*[[https://drive.google.com/file/d/10Wnoxwbb0AwRnKSVLAeHA_fzdUSQiUtf|Záznam Cv. 31.3.2021]] */ - ** Real data analysis - spike sorting | //Analýza reálných dat - Spike sorting// ** * 10.4.2024 * //Assignment: Exercise 2.3// * [[https://drive.google.com/file/d/1bTK7OJaryjUSuPo2uvVWCbSRRuUb60nn/view | Ex. 2.3 - video tutorial]] (43 min) * {{:courses:a6m33nin:tutorials:cv7_spikesorting_data.mat |cv7_spikesorting_data.mat}} * {{ :courses:beam33nin:tutorials:cv7_amp_detect.m |cv7_amp_detect.m}} * [[https://drive.google.com/file/d/1E8wu4hzncbJnBuG-Lf3ARCJgPjfVrIAR/view?usp=drive_link| Recorded lab 08/2024]] - ** Real data analysis - eye movements | //Analýza reálných dat - okohybné pohyby//** * 17.4.2024 * //Assignment: Exercise 2.4// * [[https://drive.google.com/file/d/10L70yg9PzrrdRDnPIYCgsUW-al6H9ZWz/view?usp=sharing | Ex. 2.4 - video tutorial]] (11 min) * {{ :courses:a6m33nin:tutorials:cv8_eogdata.mat |cv8_eogdata.mat}} * [[https://drive.google.com/file/d/1k68Shyn-9krx8oBgUjOV3AzqbgEbcjFY/view?usp=drive_link|Recorded lab 09/2024]] - ** Hebbian learning | //Hebbovské učení // ** * 24.4.2024 * //Assignment: Exercise 3.1// * [[https://drive.google.com/file/d/1IA2k7JzOxl76w3W2q7p-G_pnV-KLEsLP|Ex. 3.1 - video tutorial]] (26 min) * [[https://drive.google.com/file/d/1wdt5RhxNeeSeTk4tlbrxmQKtjg3CVk-T/view?usp=drive_link|Recorded lab 10/2024]] - ** Public holidays | // SVÁTEK // ** * 1.5.2024 - ** Spiking networks | //Spontánní aktivita neuronových sítí// ** * **9.5.2024 - Thursday!** * //Assignment: Exercise 3.2// * [[https://drive.google.com/file/d/1FsBlQ9sScLmvq8T3WX7AT8r4sJB-OxVO|Ex. 3.2 - video tutorial]] (4 min) * [[https://drive.google.com/file/d/1HqV-Ydac1OjiYJlgGAkpVCBCrlvcJv3N/view?usp=drive_link|Recorded lab 11/2024]] - ** Self-organizing maps | //Samoorganizující mapy// ** * //Assignment: Exercise 3.3// * 15.5.2024 * //[[https://drive.google.com/file/d/12eGurkQEg_EFerC9TDIwl00Hubsb0xg0/view | Ex. 3.3 - video tutorial]] (32 min)// * {{ :courses:bam33nin:tutorials:cv11_vowel_data.zip |vowel data mirror}} - ** Hand-in of remaining assignments, assessment//odevzdání zbývajících úloh, zápočet// ** * 22.5.2024 ====== Kontakty | Contacts ====== Přednášející | //Lecturer//: [[xnovakd1@labe.felk.cvut.cz|Daniel Novák]] /*, [[vavrecka@fel.cvut.cz|Michal Vavrečka]]*/ Cvičící | Labs TAs: [[bakstedu@fel.cvut.cz|Eduard Bakštein]] /* , [[stepakar@fel.cvut.cz|Karla Štěpánová]] ,[[vavrecka@fel.cvut.cz|Michal Vavrečka]] */ Konzultace po individuální e-mailové domluvě s cvičícím / //Consultations possible upon email request to the TAs// [[https://cw.felk.cvut.cz/forum|Fórum]]