Macro Programming in ImageJ, Oct 18th

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 (

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).

Join us!

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 if you are interested!

See you soon!

Deep Learning Workshop, June 10-12th

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.

Ephys and optogenetics workshop, April 24 – 26th

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:

Mitra Javadzadeh is a PhD student in the Hofer lab at Sainsbury Wellcome Centre. She is interested in the long range communication between cortical visual areas. She employs in vivo multi-area simultaneous electrophysiological recordings and optogenetic perturbations. in her work

Mathias Mahn is a postdoc in Andreas Luthi Lab at Friedrich Miescher Institute. He likes tinkering with proteins, light, and electronics to get a better grasp of the interactions between brain areas. Currently he is looking into the influence of amygdala activity on cortical processing. Before that, he spent most of his days designing or characterizing light-gated proteins for neuronal inhibition in Ofer Yizhar’s lab at the Weizmann Institute.

Ivan Voitov is a PhD student in the lab of Prof. Thomas Mrsic-Flogel at Sainsbury Wellcome Centre. He is interested in the function of cortico-cortical loops. He uses in vivo methods of 2-photon calcium imaging and extracellular electrophysiology while the mice perform a behavioural task designed to dynamically engage visual working memory .

Kacper Kondrakiewicz is a PhD student in Laboratory of Emotions Neurobiology, Nencki Institute. He works on social coordination of behavior in rodents. He is interested in behavioral and computational neuroscience. .

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.

Braitenberg vehicles and Arduino – how to make a robot

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.


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.

Using git for scientific software projects, February 15th

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.


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.

Introduction to Software Engineering for Scientists, February 25-26th

The aim of the workshop is to improve coding skills of its participants to include software engineering techniques. Participants will learn a new way of thinking about their code, as well as some useful techniques and tips. After the workshop, the participant will be able to write more reliable, readable and reusable code, and in consequence to make their research more reproducible. The workshop IS NOT intended as a course of any particular software development tool though. 

Day 1 (4-5h of lectures): 

  •     programming paradigms (OOP, structured and functional),
  •     good programming practices,
  •     SOLID principles.

Day 2 (~1h of programming exersises, ~3-4h of lectures): 

  •     Test Driven Development,
  •     Mocking,
  •     Tutorial Driven Documentation (optional)


  •     intermediate proficiency in programming (Python recommended),
  •     a device with Anaconda Python installed (2nd day),
  •     Polish proficiency may make your 2nd day experience funnier;-).

Please find the application form here. We wait for applications until February 20th.


IMG_0187-US Wiza (format cyfrowy)-900x900 px.jpgJakub Dzik is a scientific programmer working in the laboratory of Neuroinformatics, Nencki Institute, where he is developing software tools for scientific use. Striving to improve research reproducibility by delivering code that is reliable and easy to manage, I have learned the basics of software engineering.

3D printing workshop, January 26th

We have a pleasure to announce our next workshop on 3D printing!

Additive manufacturing, commonly known as 3D printing is a rapidly developing subfield of fabrication. Unprecedented versatility and constant decrease of prices of both the software and the hardware contribute to the growing popularity of 3D printing. Ability to create and at hand manufacture almost any objects needed may greatly improve capacity and cost-effectiveness of development of highly customised experimental setups. We would like to present the possibilities and limitations of the academic applications of 3D printing.


During the workshop participants will be acquainted with an overview of 3D printing technologies, construction of FDM printers and workflow of design, printing and postprocessing of desired objects.

 Please find the application form here. We are waiting for the applications till January  13th.


Deep Lab Cut Workshop, December 13-14th

Photo from


We would like to invite you to the workshop about Deep Lab Cut Software with dr Alexander Mathis (Bernstein Centre for Computational Neuroscience, Tuebingen, Harvard University).

 Deep Lab Cut is an open-source software based on transfer learning with deep neural networks, allowing very precise and efficient tracking of the body parts of the animal (from Drosophila to human). It can be used to track e.g. single whiskers of the mouse, body parts of the rat in the open maze test, human hand movements and more.

Tracking of the electric fish body parts (by Avner Wallach) and human hand movements (by James Bonajuto)


More about the software can be found here . 

Participation in the workshop is free. Basic knowledge of Python is required. Please find the application form hereWe are waiting for the applications till November 29th.



Teaching Assistants:

 Alexander Mathis

Is a postodoctoral fellow in the lab of Matthias Bethge at the Bernstein Center for Computational Neuroscience in Tuebingen and the University of Tuebingen and the lab of Venkatesh N. Murthy at the Department of Molecular and Cellular Biology at Harvard University. He is interested in in odor-guided navigation, pose estimation as well as motor control and adaptation.

Bonsai Workshop


We would like to invite you to the first workshop about Bonsai programming language with Nacho Sanguinetti from Bernstein Centre for Computational Neuroscience

Bonsai is an open visual programming language used in neuroscience for the development of behavioural paradigms. You can use Bonsai to track an animal, deliver visual or auditory stimuli and combine it with Arduino to control lasers, automated doors, 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 animal will be tracked online and the cage environment will change – the door will open, the light will be switched and the sound produced depending on animal’s position and behaviour.             You will learn also the basics of 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.              We also plan an integration session on Tuesday, November 22nd!

Please find a registration form here .


The workshop will take place 10AM – 2PM each day in the Department of Physics, Warsaw University. 


 Juan Ignacio Sanguinetti 

(Bernstein Center for Computational Neuroscience, Berlin) has graduated from University of the Republic, Montevideo (Uruguay) has strong background in behavioural studies, including work on electric fish and mice. Currently he works as a post-doc in the lab of Michael Brecht in Bernstein Center for Computational Neuroscience, Berlin. He combines behavioural techniques with in vivo electrophysiological recordings.