Open Source Software seminars

OpenSPM aims to democratize innovation in the field of scanning probe microscopy (SPM), which is currently dominated by a few proprietary, closed systems that limit user-driven development. Our platform includes a high-speed OpenAFM head and base optimized for small cantilevers, an OpenAFM controller, a high-voltage amplifier, and interfaces compatible with several commercial AFM systems such as the Bruker Multimode, Nanosurf DriveAFM, Witec Alpha SNOM, Zeiss FIB-SEM XB550, and Nenovision Litescope. We have created a fully documented and community-driven OpenSPM platform, with training resources and sourcing information, which has already enabled the construction of more than 15 systems outside our lab. The controller is integrated with open-source tools like Gwyddion, HDF5, and Pycroscopy. We have also engaged external companies, two of which are integrating our controller into their products or interfaces. We see growing interest in applying parts of the OpenSPM platform to related techniques such as correlated microscopy, nanoindentation, and scanning electron/confocal microscopy. To support this, we are developing more generic and modular software, alongside a structured development workflow. A key feature of the OpenSPM system is its Python-based API, which makes the platform fully scriptable and ideal for AI and machine learning applications. This enables, for instance, automatic control and optimization of PID parameters, setpoints, and experiment workflows. With a growing contributor base and industry involvement, OpenSPM is well positioned to become a global, open platform for next-generation SPM innovation.

When meta-research (research on research) makes an observation or points out a problem (such as a flaw in methodology), the project should be repeated later to determine whether the problem remains. For this we need meta-research that is reproducible and updatable, or living meta-research. In this talk, we introduce the concept of living meta-research, examine prequels to this idea, and point towards standards and technologies that could assist researchers in doing living meta-research. We introduce technologies like natural language processing, which can help with automation of meta-research, which in turn will make the research easier to reproduce/update. Further, we showcase our open-source litmining ecosystem, which includes pubget (for downloading full-text journal articles), labelbuddy (for manually extracting information), and pubextract (for automatically extracting information). With these tools, you can simplify the tedious data collection and information extraction steps in meta-research, and then focus on analyzing the text. We will then describe some living meta-research projects to illustrate the use of these tools. For example, we’ll show how we used GPT along with our tools to extract information about study participants. Essentially, this talk will introduce you to the concept of meta-research, some tools for doing meta-research, and some examples. Particularly, we want you to take away the fact that there are many interesting open questions in meta-research, and you can easily learn the tools to answer them. Check out our tools at https://litmining.github.io/

Edmund will present why to use FPGAs when building scientific instruments, when and why to use open source FPGA tools, the history of their development, their development status, currently supported FPGA families and functions, current developments in design languages and tools, the community, freely available design blocks, and possible future developments.

It is now widely accepted that openness and transparency are keys to improving the reproducibility of scientific research, but many challenges remain to adoption of these practices. I will discuss the growth of an ecosystem for open science within the field of neuroimaging, focusing on platforms for open data sharing and open source tools for reproducible data analysis. I will also discuss the role of the Brain Imaging Data Structure (BIDS), a community standard for data organization, in enabling this open science ecosystem, and will outline the scientific impacts of these resources.

Cognitive neuroscience has witnessed great progress since modern neuroimaging embraced an open science framework, with the adoption of shared principles (Wilkinson et al., 2016), standards (Gorgolewski et al., 2016), and ontologies (Poldrack et al., 2011), as well as practices of meta-analysis (Yarkoni et al., 2011; Dockès et al., 2020) and data sharing (Gorgolewski et al., 2015). However, while functional neuroimaging data provide correlational maps between cognitive functions and activated brain regions, its usefulness in determining causal link between specific brain regions and given behaviors or functions is disputed (Weber et al., 2010; Siddiqiet al 2022). On the contrary, neuropsychological data enable causal inference, highlighting critical neural substrates and opening a unique window into the inner workings of the brain (Price, 2018). Unfortunately, the adoption of Open Science practices in clinical settings is hampered by several ethical, technical, economic, and political barriers, and as a result, open platforms enabling access to and sharing clinical (meta)data are scarce (e.g., Larivière et al., 2021). We are working with clinicians, neuroimagers, and software developers to develop an open source platform for the storage, sharing, synthesis and meta-analysis of human clinical data to the service of the clinical and cognitive neuroscience community so that the future of neuropsychology can be transdiagnostic, open, and FAIR. We call it neurocausal (https://neurocausal.github.io).

Large-scale numerical simulations of brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. Similarly, spiking neural networks are also gaining traction in machine learning with the promise that neuromorphic hardware will eventually make them much more energy efficient than classical ANNs. In this session, we will present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale spiking neuronal networks to address the challenge of efficient simulations. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. GeNN was originally developed as a pure C++ and CUDA library but, subsequently, we have added a Python interface and OpenCL backend. We will briefly cover the history and basic philosophy of GeNN and show some simple examples of how it is used and how it interacts with other Open Source frameworks such as Brian2GeNN and PyNN.

We introduce Norse: An open-source library for gradient-based training of spiking neural networks. In contrast to neuron simulators which mainly target computational neuroscientists, our library seamlessly integrates with the existing PyTorch ecosystem using abstractions familiar to the machine learning community. This has immediate benefits in that it provides a familiar interface, hardware accelerator support and, most importantly, the ability to use gradient-based optimization. While many parallel efforts in this direction exist, Norse emphasizes flexibility and usability in three ways. Users can conveniently specify feed-forward (convolutional) architectures, as well as arbitrarily connected recurrent networks. We strictly adhere to a functional and class-based API such that neuron primitives and, for example, plasticity rules composes. Finally, the functional core API ensures compatibility with the PyTorch JIT and ONNX infrastructure. We have made progress to support network execution on the SpiNNaker platform and plan to support other neuromorphic architectures in the future. While the library is useful in its present state, it also has limitations we will address in ongoing work. In particular, we aim to implement event-based gradient computation, using the EventProp algorithm, which will allow us to support sparse event-based data efficiently, as well as work towards support of more complex neuron models. With this library, we hope to contribute to a joint future of computational neuroscience and neuromorphic computing.

FED3 is a device for behavioral training of mice in vivarium home-cages. Mice interact with FED3 through two nose-pokes and FED3 responds with visual stimuli, auditory stimuli, and by dispensing pellets. As it is used in the home-cage FED3 can be used for around-the-clock training of mice over several weeks. FED3 is open-source and can be built by users for ~10-20x less than commercial solutions for training mice. The control code is also open-source and was designed to be easily modified by users.

Modern biological methods often require a large number of experiments to be conducted. For example, dissecting molecular pathways involved in a variety of biological processes in neurons and non-excitable cells requires high-throughput compound library or RNAi screens. Another example requiring large datasets - modern data analysis methods such as deep learning. These have been successfully applied to a number of biological and medical questions. In this talk we will describe an open-source platform allowing such experiments to be automated. The platform consists of an XY stage, perfusion system and an epifluorescent microscope with autofocusing. It is extremely easy to build and can be used for different experimental paradigms, ranging from immunolabeling and routine characterisation of large numbers of cell lines to high-throughput imaging of fluorescent reporters.