- Practical Guide
- About Neuronus
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:
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 firstname.lastname@example.org.
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.
QuPath  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,
-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  using the ABBA  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 email@example.com.
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.
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.
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 firstname.lastname@example.org.
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.