Activities

Workshops and Networking

Workshops: 24 April '24

Workshop 1. Neuropixels

In order to meet the need for single spike resolution recordings of vast populations of neurons dispersed throughout different brain areas, neuropixel probes have been developed. They were created by Tim Harris's Neuropixels consortium.

The ability to provide a greater signal to noise ratio, unit yield, cluster fidelity, and channel count are among the primary characteristics of neuropixel probes. These days, a wide variety of species, including mice, rats, ferrets, and non-human/human primates, employ neuropixel probes for a variety of purposes.

Today, the majority of Neuropixels customers put one or more probes into the same brain on an experimental day and conduct acute recordings in animals with head restraints. Acute Neuropixels probe recordings are remarkably scalable, as demonstrated by the simultaneous recording of several hundreds of neurons in numerous brain areas using two to three probes.

Nonetheless, a lot of well-known behavioral paradigms need that animals be allowed to move freely throughout an experiment. Furthermore, studies on the learning of complicated behaviors necessitate the acquisition of the same neuronal population over a period of days, which can be accomplished through the use of chronic preparations. Furthermore, long-term planning may be crucial in tracking the advancement of brain disorders.

Being experienced users at Neuroelectronics Research Flanders, we have created a range of fixtures that make it easier to implant Neuropixel probes over an extended period of time.

Using these plug-and-play fixtures, we were able to measure neural activity from the same animal on a daily basis. Crucially, our methodology permits the cost-effective recovery of implanted probes for re-implantation in different indviduals at a later time. Hence, the application of Neuropixels probes in freely moving animals could be expanded thanks to our chronic Neuropixels procedure. It may also take the place of acute preparations in certain cases since it avoids several of its main drawbacks, including the requirement for an open craniotomy, the possibility of bleeding, and acute tissue compression.

During the workshop we will:

  • go over the neuropixels technology from 1.0 to 2.0
  • fly over previously established neuropixels chronic preparations and I would like to give an essence about where we at the moment.
  • perform hands on workshop to prepare chronic fixtures with dummy neuropixels probes
  • learn how to analyze data that is acquired using neuropixels 2.0 probes

The workshop is open for Neuropixels users at any stage of experience (want-to-use, beginners, profis) for intensifying the exchange among local users.

To maintain high efficiency of the workshop, max. 20 participants will be allowed to attend.

Applicants should provide a 1-page motivation letter describing their background and explaining the acute and long-term needs of using neuropixels (or related approaches). Please submit the letter via email neuronusforum@uj.edu.pl

The workshop will be led by one of the main developers of chronic neuropixels fixtures, Cagatay Aydin. Cagatay has a background in engineering and received his PhD in molecular and cognitive neuroscience at KU Leuven (Belgium) in 2019. He contributed to both Neuropixels 1.0 and 2.0 papers and he is currently one of the tutors in neuropixels workshop at Allen Institute since 2000.

Workshop 2. QuPath

QuPath [1] is an open-source bioimage analysis software. It is generally used for digital pathology applications for which it offers a powerful set of tools to operate on whole-slide images, but it can be used with many other types of histological images as well. 

In our facility, we mainly use QuPath for (a) the precise classification and delineation of 2D tissue as a crucial step in detecting pathological vs. healthy tissue (e.g. cancer and stroma regions), and (b) cell detection in defined tissue regions of interest, including the quantification of cell numbers, densities, and positivity rates of multiple biomarkers. We perform such analyses on histological scans and multi-channel image series with up to ~40 immunohistological protein markers.

During this 6-hour interactive workshop, you will learn:
-how to visualize images,
-annotate objects,
-create pixel classifiers,
-detect and classify objects in order to extract quantitative data.
The workshop will be based on a data set consisting of mouse brain slices registered to the Allen brain atlas [2] using the ABBA [3] extension.

To maintain high efficiency of the workshop, max. 20 participants will be allowed to attend. Applicants should provide a 1-page motivation letter describing their background and explaining the acute and long-term needs of using QuPath (or related approaches). Please submit the letter via email neuronusforum@uj.edu.pl

The workshop will be led by Ewelina Bartoszek. Ewelina is a senior staff member at the DBM Microscopy Core Facility in Basel, Switzerland. Her main focus is on bio-image analysis. Ewelina actively engages in the bioimage community, serving as a board member of SwissBIAS and a co-organizer of the ZIDAS summer school where she co-host a QuPath course.

Workshop 3. DeepLabCut and pose estimation data analysis workshop

With the rapid emergence of new, easily available machine learning tools and a push towards automation, it's essential not only to use them but also to do so correctly and competently, with at least some understanding of their inner workings. This workshop, designed for individuals with a basic understanding of DLC workflow, will be conducted as a hands-on session where participants can work on their data under the guidance of an instructor. 

The workshop will consist of three parts:
1) Theoretical introduction to key concepts in machine learning and their relevance to DLC, including an overview of hyperparameters.
2) Practical session: Participants will work on their own data, asking questions, refining their models, selecting appropriate tracking parameters, and filtering and cleaning the output data.
3) Introduction to pose estimation data analysis: Participants will learn how to navigate DLC's multi-indexed output, calculate kinematics, analyze interactions between animals, and explore existing tools for further analysis of DLC output.

To maintain high efficiency of the workshop, max. 20 participants will be allowed to attend. Applicants should provide a 1-page motivation letter describing their background and explaining the acute and long-term needs of using DeepLabCut (or related approaches). Please submit the letter via email neuronusforum@uj.edu.pl

The workshop will be led by Konrad Danielewski.Konrad is a PhD student at Knapska's Lab within Nencki PAS in Warsaw. His research focuses on the encoding of behavioral information from self and others in the rat's medial prefrontal cortex. Konrad is a long time DeepLabCut project contributor and collaborator being invested in the project and its community for over four years. In 2023 he was awarded a scholarship to become a DLC AI Resident - a program during which he worked closely with the DLC team on new version of DLC and new community resources.

We will soon be announcing more workshops and networking events!
REGISTRATION FOR WORKSHOPS!
To maintain high efficiency of the workshops, max. 20 participants will be allowed to attend to each workshop! The workshops will be held on 24 April '24 in parallel, at the same time. Therefore, you can only register for one workshop.
Registration is done via email neuronusforum@uj.edu.pl byFebruary 14February 28.

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