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DeepLabCut is a pose estimation framework developed in Mackenzie Mathis Lab, used to track arbitrarily selected body parts of an animal from your video data. Aim of this workshop will be to learn how to use DeepLabCut in multianimal pose estimation and what to do with the data.

We will be creating a project either on provided or own data and will go through the whole workflow, closely examining the most important steps, trying to overcome the most common new user hurdles as well as built upon our knowledge from previous DLC workshops. We will also cover basics of DLC tracking data analysis: ROI analysis, measurment of thedistance covered by an animal and its velocity.

To take part in our workshop, all you’ll need is a laptop (Windows, Linux, MacOS are all fine). All instructions on how to install necessary software will be provided before the workshop and participants are expected to have everything installed on the day of the workshop – contact k.danielewski@nencki.edu.pl in case of any issues. Participants without previous experience with DLC are most welcome!

Workshop will take place Sept 23th at 10 AM in Nencki Institute. Please find the application form here.

TA:

Konrad Danielewski is a PhD student in Knapska Laboratory. He is interested in using machine learning methods for behavioural data analysis. He is a member of Deep Lab Cut team.

We are happy to announce our new workshop – Behavioral experiment design with Bonsai and Arduino.

Bonsai is an open visual programming language used in neuroscience for the development of behavioural paradigms with animal and human subjects. You can use Bonsai to track an animal with a camera, deliver visual or auditory stimuli, create virtual reality and combine it with Arduino to control lasers, automated doors, stimulus delivery systems and synchronize different setups – and many, many more. 

More about Bonsai can be found here.

The aim of the workshop will be to develop a closed – loop behavioural paradigm, in which a robot will be tracked and the environment will change depending on its behavior. You will learn the basics of Bonsai and Arduino programming. During the last day of the project, you will be also able to discuss your ideas and ask us how to implement skills from the workshop in your everyday research practice.      

 
Please find a registration form here .

Contact: nenckiopenlab@gmail.com

The workshop will take place 10AM – 3 PM each day. The fee is 120 PLN.

We are happy to announce the second edition of our ImageJ workshop!

ImageJ is an open source image processing software designed for scientific image analysis. Its most often used distribution is called Fiji. This software has a lot of built-in functions and plugins. ImageJ has its own programming language based on Java. As scientists, we often want to perform image analysis on large datasets (detecting hundreds of particles on hundreds of images). If you don’t want to click the dots for all eternity, writing a macro is the perfect solution.

During this workshop you will learn how to automate some of your analyses by writing simple macros in ImageJ. Prerequisites for this workshop are basic skills in any programming language as well as basic knowledge of what ImageJ can do.

Workshop will take place June 11th, 11AM – 3 PM. Please find the application form HERE. We wait for applications until May 20 th. The cost of the workshop is 60 PLN.

Please install Fiji before workshop (https://fiji.sc/).

Kacper Łukasiewicz PhD, is a postdoctoral scholar in the Zuo Laboratory, MCD Biology, University of California, Santa Cruz. During his PhD in the Laboratory of Molecular Basis of Behavior in Nencki Institute he worked on alcohol-induced memory impairment and analyzed hundreds of images from immunostainings (and saved hundreds of hours using ImageJ macros for this).

Basic knowledge in electronics is necessary prerequisite for every neuroscientist. You will need it to build your own amplifier to record a sniffing pattern of a mouse; it will allow you to fully understand how is your electrophysiological setup working and to appreciate what is really happening inside of a cell during an action potential.

This workshop is intended to provide you with theoretical and practical knowlege about electronics – from Ohm’s law to basics of computer logic. The topics covered will include:

• Theoretical introduction – current, voltage, resistance, Ohm’s Law, Kirchoff’s laws
• Basic tools in electronics – multimeters, oscilloscopes
• Resistors, diodes, capacitors
• Analog sensors, motors, servos
• Amplifiers
• Transistors, switches, logic gates, integrated circuits (how computers work?)

Participants will receive kits with all the necessary elements; the workshop will be focused on practical exercises.

The cost of the workshop is 70 PLN. You can find the application form HERE.

Workshop will be organized between 9AM – 3 PM.

TAs:

Mateusz Kostecki is a PhD student in Nencki Institute. He works on social transmission of information in rodents; he is interested in nervous system evolution, electronics and robotics.

Ula Włodkowska Ula Włodkowska is a PhD student in Spatial Memory Lab at Nencki. She works on spatial engram evolution at different time points during learning and changes in involvement of hippocampal-cortical interactions throughout the process. A former software developer, she is interested in computational neuroscience, electronics and IoT.

ImageJ is an open source image processing software designed for scientific image analysis. Its most often used distribution is called Fiji. This software has a lot of built-in functions and plugins. ImageJ has its own programming language based on Java. As scientists, we often want to perform image analysis on large datasets (detecting hundreds of particles on hundreds of images). If you don’t want to click the dots for all eternity, writing a macro is the perfect solution.

During this workshop you will learn how to automate some of your analyses by writing simple macros in ImageJ. Prerequisites for this workshop are basic skills in any programming language as well as basic knowledge of what ImageJ can do.

Workshop will take place October 18th, 10AM – 3 PM. Please find the application form here. We wait for applications until Oct 10 th. The cost of the workshop is 60 PLN.

Please install Fiji before workshop (https://fiji.sc/).

Kacper Łukasiewicz recently finished his PhD in the laboratory of Molecular Basis of Behavior, Nencki Institute. During his PhD he worked on alcohol-induced memory impairment and analyzed hundreds of images from immunostainings (and saved hundreds of hours using ImageJ macros for this).

As our Nencki Open Lab project is dynamically developing, we are currently looking for PhD students and other scientists Ochota Campus who would like to join us!

Our plans for the following year include: workshops: i.a. Matlab programming, optics (we plan to build a fluorescent microscope from scratch!), 3D printing, analysis of behavioural data, Arduino, electronics, LaTeX and others; the next edition Nencki Open Lab Summer School on Behavioral Neuroscience and weekly seminars.

There are many ways in which you can contribute to the project:

• organizing workshops – preparing announcements, spreading information about workshops on social media, taking care of workshop logistics
• organizing weekly seminars – inviting speakers, spreading the news
• organizing Nencki Open Lab Summer School

Organizational meeting will take place October 2nd, 3:00 PM at Nencki. Please write to us at nenckiopenlab@gmail.com if you are interested!

See you soon!

We would like to invite you to the lat workshop this year!

Deep Neural Networks have many successful applications in the recent past among which there are: objects recognition, language understanding, robotic or car movement and many more. They also grow a lot of public attention which leads to many unrealistic expectations and misunderstandings.

During the workshop we will present a theoretical basis of Deep Neural Networks as well as a simple yet powerful way of creating such networks which will be capable of object and pattern recognition as well as learning from the reinforcement feedback.

All algorithms will be explained so that the participants can easily understand what are the basics of the artificial neural network and what are the main challenges during the development.

We recommend that participants should have a basic knowledge of Python programming. Workshop will take lace June 10-12th. The deadline for application is May 30th, application form can be found here.

Workshops will start 10 AM and last till 6 PM.

Wladyslaw Sredniawa

MS in Biomedical Physics and Molecular Biology. PhD student of the Warsaw University involved in neuroinformatics projects including multielectrode signal analysis, biological neural networks modeling and performing neurobiological experiments. Experienced teacher in basic programming in Python.

Ziemowit Slawinski

PhD student of the Nencki Institute in the laboratory of Neuroinformatics. Deep Neural Networks researcher for companies such as: Hoffmann La Roche and Samsung Research Institute. Experienced in creating artificial neural networks for: language understanding and generation, reinforcement feedback learning and object recognition. Currently working on simulations of calcium dynamics driven by neuron’s electrical activity and calcium/calmodulin activated signalling pathway.

We have pleasure to announce the next Nencki Open Lab Workshop!

This time you will have an oportunity to learn about electrophysiological recordings and optogenetics. During the workshop we will go from basics (neuron biophysics, ion channels the design of the ephys setup) to practicals – building tetrodes and optic cannulas, using Arduino to control your optogenetic stimulation protocols, ephys data analysis and intepretation. We will discuss how to synchronize diffrent data streams and combine your recordings and stimulation with behavioral experiments.

During the workshop you will also have an unique opportunity to discussing your ideas and problems with experts!

Workshop will take place April 24-26th. You can find an application form here .

The cost of the workshop is 50 PLN. The deadline for applications is April 18th.

Teaching Assistants:

In a now classic book, Valentino Braitenberg described a thought experiment in which, by building simple robots with motors and sensors we can obtain a set of machines exhibiting surprisingly complex behavioural repertoire. Braitenberg vehicles „love” or „hate” objects in their environment, they can learn new things and, to an observer, seem to be really intelligent creatures.

The book shows how complex behaviors can be generated by simple mechanisms and create a great starting point for thinking about animal behavior and the function of the nervous system.

In our next workshop, we will use Arduino to build robots inspired by Braitenberg vehicles. Our machines will search for light or avoid it, will detect obstacles, exhibit „feelings” towards other robots and many more. We will illustrate each of our vehicles with analogous mechanisms that can be found in real living systems, from bacteria to animals.

Beyond that, our workshop will be a great introduction to Arduino robotics. You will learn how to write and organize more complex Arduino code and how to combine many sensors with many effectors in an efficient way, how to use more advanced libraries and communication protocols.

Workshop will take place March 23-24th (weekend), 9AM – 4 PM. Please find the application form here. We wait for applications until March 12th.

We require a basic experience with Arduino programming.

The cost of the workshop is 50 PLN.

Tutor:

Mateusz Kostecki is a PhD student in Nencki Institute. He works on social transmission of information in rodents; he is interested in nervous system evolution, developmental psychobiology and robotics.

During workshop we will cover all the basic elements of how the code is nowadays managed using the open infrastructure provided by GitHub and the free CI runners. You will learn how to set up a repository so that others can contribute to it by sending pull requests, and to have the pull requests automatically tested.

Plan of the workshop:

– quick introduction to version control using git
– testing scientific code and using CI systems
– the OSS workflow using public code, branches, pull requests, and review

Please find the application form here. We wait for applications until February 11th.

Tutor:

Zbigniew Jędrzejewski-Szmek has a PhD in molecular physics and experience with development of both scientific and non-scientific open-source software. After 10 years of working as a scientist and a scientific programmer, he is currently working for Red Hat.