Biology subjects

Diederich, B.

Publications and source records attributed to Diederich, B..

10 recordsLinked to original sources

bioRxiv2025

Smart Microscopy: Current Implementations and a Roadmap for Interoperability

Smart microscopy is transforming life sciences by automating experimental imaging workflows and enabling real-time adaptation based on feedback from images and other data streams. This shift increases throughput, improves reproducibility, and expands the functional capabilities of microscopes. However, the current landscape is highly fragmented. Academic researchers often develop custom solutions for specific scientific needs, while industry offerings are typically proprietary and tied to specific hardware. This diversity, while fostering innovation, also creates major challenges in interoperability, reproducibility, and standardization, which slows progress and adaption. This article presents a collaborative effort between academic and industry leaders to survey the current state of smart microscopy, highlight representative implementations, and identify common technical and organizational barriers. We propose a framework for greater interoperability based on shared standards, modular software design, and community-driven development. Our goal is to support collaboration across the field and lay the groundwork for a more connected, reusable, and accessible smart microscopy ecosystem. We conclude with a call to action for researchers, hardware developers, and institutions to join in building an open, interoperable foundation that will unlock the full potential of smart microscopy in life science research.

cell biology↗

bioRxiv2025

Chromatix: a differentiable, GPU-accelerated wave-optics library

Modern microscopy methods incorporate computational modeling as an integral part of the imaging process, either to solve inverse problems or optimize the optical system design itself. These methods often depend on differentiable optics simulations, yet no standardized framework exists--forcing computational optics researchers to repeatedly and independently implement simulations with limited reusability and performance. These common problems limit the potential impact of computational optics as a field. Here we present Chromatix: an open-source, GPU-accelerated, differentiable wave optics simulation library. Chromatix builds on JAX to democratize fast, parallelized simulation of diverse optical systems and expand the design space in computational optics. Chromatix standardizes a growing collection of optical elements and propagation methods allowing a broad range of applications, which we demonstrate here for snapshot microscopy, holography, and phase retrieval. We demonstrate speed improvements of 2-6x on a single GPU and up to 22x on 8 GPUs.

bioinformatics↗

bioRxiv2024

Fully-Automated Multicolour Structured Illumination Module for Super-resolution Microscopy

In the rapidly advancing field of biological imaging, there is a great need for high-resolution imaging techniques that are both cost-effective and accessible, for example to better observe and understand dynamics in intracellular processes. Structured illumination microscopy (SIM) is the method of choice to achieve high axial and lateral resolution in living samples due to its optical sectioning and minimal phototoxicity. However, the high cost and complexity of conventional SIM systems limit their wide application. In our work, we present an open-source, fully-automated, two-color structured illumination module that is compatible with commercially available microscope stands. The compact design, consisting of low-cost single-mode fiber-coupled lasers and a digital micromirror device (DMD), is integrated into the open-source acquisition and control software (ImSwitch) in order to realize real-time super-resolution imaging. This developed system achieves up to a 1.55-fold improvement in lateral resolution compared to conventional wide-field microscopy. To rationally design this module, we developed a model to ensure optimal DMD diffraction per-formance using tilt and roll pixels, thus covering a wide range of low-cost video projectors for use in coherent SIM setups. Our goal is to democratize SIM-based super-resolution microscopy by providing both comprehensive open-source documentation and a modular software framework that works with various hardware components (e.g. cameras, stages) and reconstruction algorithms. In this way, we try to upgrade as many devices as possible to the super-resolution realm.

cell biology↗

bioRxiv2024

ESPressoscope: a small and powerful platform for in situ microscopy

Microscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We address this challenge by investigating the feasibility of using a simple microcontroller board not only as a portable and field-ready digital microscope, but furthermore as a versatile platform which can easily be adapted to a variety of imaging applications. By adding a few external components, we demonstrate that a low-cost ESP32 camera board can be used to build an autonomous in situ platform for digital time-lapse imaging of cells. This platform, which we call the ESPressoscope, can be adapted to applications ranging from monitoring incubator cell cultures in the lab to observing ecological phenomena in the sea, and it can be adapted for other techniques such as microfluidics or spectrophotometry. The ESPressoscope achieves a low power consumption and small size, which makes it ideal for field research in environments and applications where microscopy was previously infeasible. Its Wi-Fi connectivity enables integration with external image processing and storage systems, including on cloud platforms when internet access is available. Finally, we present several web browser-based tools to help users operate and manage the ESPressoscopes software. Our findings demonstrate the potential for low-cost, portable microscopy solutions to enable new and more accessible experiments for biological and analytical applications.

microbiology↗

bioRxiv2023

An open-source, high resolution, automated fluorescence microscope

Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.

cell biology↗

bioRxiv2021

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

The number of samples in biological experiments are continuously increasing, but complex protocols and human experimentation in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments and due to lack of open APIs they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, we demonstrate automated, high-throughput experiments for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools Openflexure, Opentrons, ImJoy and UC2. Our automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on analysis of previously acquired images, enables the realization of smart microscopy experiments, featuring completely autonomously performed experiments. All documents and source-files are publicly available (https://beniroquai.github.io/Hi2) to prove the concept of smart lab automation using inexpensive, open tools. We believe this democratizes access to the power and repeatability of automated experiments.

cell biology↗

bioRxiv2021

UCsim2: 2D Structured Illumination Microscopy using UC2

State-of-the-art microscopy techniques enable the imaging of sub-diffraction barrier biological structures at the price of high-costs or lacking transparency. We try to reduce some of these barriers by presenting a super-resolution upgrade to our recently presented open-source optical toolbox UC2. Our new injection moulded parts allow larger builds with higher precision. The 4x lower manufacturing tolerance compared to 3D printing makes assemblies more reproducible. By adding consumer-grade available open-source hardware such as digital mirror devices (DMD) and laser projectors we demonstrate a compact 3D multimodal setup that combines image scanning microscopy (ISM) and structured illumination microscopy (SIM). We demonstrate a gain in resolution and optical sectioning using the two different modes compared to the widefield limit by imaging Alexa Fluor 647- and SiR-stained HeLa cells. We compare different objective lenses and by sharing the designs and manuals of our setup, we make super-resolution imaging available to everyone.

cell biology↗

bioRxiv2020

Nanoscopy on the Chea(i)p

Super-resolution microscopy allows for stunning images with a resolution well beyond the optical diffraction limit, but the imaging techniques are demanding in terms of instrumentation and software. Using scientific-grade cameras, solid-state lasers and top-shelf microscopy objective lenses drives the price and complexity of the system, limiting its use to well-funded institutions. However, by harnessing recent developments in CMOS image sensor technology and low-cost illumination strategies, super-resolution microscopy can be made available to the mass-markets for a fraction of the price. Here, we present a 3D printed, self-contained super-resolution microscope with a price tag below 1000 $ including the objective and a cellphone. The system relies on a cellphone to both acquire and process images as well as control the hardware, and a photonic-chip enabled illumination. The system exhibits 100nm optical resolution using single-molecule localization microscopy and can provide live super-resolution imaging using light intensity fluctuation methods. Furthermore, due to its compactness, we demonstrate its potential use inside bench-top incubators and high biological safety level environments imaging SARS-CoV-2 viroids. By the development of low-cost instrumentation and by sharing the designs and manuals, the stage for democratizing super-resolution imaging is set.

microbiology↗

bioRxiv2020

UC2 - A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging

With UC2 (You-See-Too) we present an inexpensive 3D-printed microscopy toolbox. The system is based on concepts of modular development, rapid-prototyping and all-time accessibility using widely available off-the-shelf optic and electronic components. We aim to democratize microscopy, reduce the reproduction crisis and enhance trust into science by making it available to everyone via an open-access public repository. Due to its versatility the aim is to boost creativity and non-conventional approaches. In this paper, we demonstrate a development cycle from basic blocks to different microscopic techniques. First, we build a bright-field system and stress-test it by observing macrophage cell differentiation, apoptosis and proliferation incubator-enclosed for seven days with automatic focussing to minimize axial drift. We prove versatility by assembling a system using the same components to a fully working fluorescence light-sheet system and acquire a 3D volume of a GFP-expressing living drosophila larvae. Finally, we sketch and demonstrate further possible setups to draw a picture on how the system can be used for reproducible prototyping in scientific research. All design files for replicating the experimental setups are provided via an open-access online repository (https://github.com/bionanoimaging/UC2-GIT) to foster widespread use.

bioengineering↗

bioRxiv2019

One-Shot phase-recovery using a Cellphone RGB Camera on a Jamin-Lebedeff Microscope

Jamin-Lebedeff (JL) polarization interference microscopy is a classical method for determining the change in the optical path of transparent tissues. Whilst a differential interference contrast (DIC) microscopy interferes an image with itself shifted by half a point spread function, the shear between the object and reference image in a JL-microscope is about half the field of view. The optical path difference (OPD) between the sample and reference region (assumed to be empty) is encoded into a colour by white-light interference. From a colour-table, the Michel-Levy chart, the OPD can be deduced. In cytology JL-imaging can be used as a way to determine the OPD which closely corresponds to the dry mass per area of cells in a single image.\n\nLike in other interference microscopy methods (e.g. holography), we present a phase retrieval method relying on single-shot measurements only, thus allowing real-time quantitative phase measurements. This is achieved by adding several customized 3D-printed parts (e.g. rotational polarization-filter holders) and a modern cellphone with an RGB-camera to the Jamin-Lebedeff setup, thus bringing an old microscope back to life.\n\nThe algorithm is calibrated using a reference image of a known phase object (e.g. optical fiber). A gradient-descent based inverse problem generates an inverse look-up-table (LUT) which is used to convert the measured RGB signal of a phase-sample into an OPD.\n\nTo account for possible ambiguities in the phase-map or phase-unwrapping artifacts we introduce a total-variation based regularization. We present results from fixed and living biological samples as well as reference samples for comparison.

bioinformatics↗