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Biology subjects

Gorelick, S.

Publications and source records attributed to Gorelick, S..

5 recordsLinked to original sources

Mind the Bend: Curved and Corrugated Cryo-Lamella for Improved Mechanical Resilience

Preparing electron-transparent cryo-lamellae is inherently a serial, low-throughput process. During sample handling, milling, and transfer, cryo-fixed cells and their supporting films are subjected to mechanical forces as well as thermal stresses caused by temperature fluctuations. After milling, these extremely thin lamellae remain vulnerable to both mechanical and thermal stress, often leading to cracking or complete disintegration. Consequently, the loss of valuable lamellae is frequently an unavoidable aspect of working with such fragile specimens. In this work, we reconsider the conventional lamella geometry, which is typically a flat, thin cross-sectional slab. During milling, lamellae often become unintentionally bent, complicating the final polishing step required to achieve uniform thinning across their width. To address this limitation, we propose deliberately fabricating lamellae in a pre-bent configuration, i.e. specifically, adopting an arch-shaped profile instead of the traditional flat geometry. The arch shape is intrinsically more mechanically stable than a flat structure, thereby reducing lamella loss due to mechanical failure. Moreover, pre-bent milling patterns facilitate uniform thinning of bent lamellae, which is difficult to achieve using conventional flat milling approaches. In addition to the arch geometry, we investigate corrugated lamellae, characterised by a sinusoidal variation around the plane of a conventional flat lamella. Similarly to the arch shape, the corrugated design offers enhanced mechanical stability compared to traditional flat lamellae. We fabricated a series of test lamellae incorporating both arches and corrugations. High-resolution cryo-TEM imaging was performed to evaluate these structures, demonstrating that non-flat geometries do not compromise cryo-electron tomography performance. Furthermore, finite element method (FEM) simulations were conducted to provide insight into stress distributions within bent and corrugated lamellae.

biochemistry↗

Mind the crack: Crack-arrest holes and soft-suspension support integration in cryo-lamella preparation for improved resistance to crack formation, fracture and deformation

Preparing electron-transparent cryo-lamellae is inherently a serial and low-throughput process. Once the lamellae are milled, these thin structures endure both mechanical and thermal stress, and as a result many valuable lamellae crack or even disintegrate entirely. This loss is often regarded as a "lamella tax", i.e. an unavoidable cost of working with such fragile specimens. In this work, we introduce two modifications to the standard lamella-preparation workflow aimed at improving lamella mechanical resistance to crack formation and external stress. The first modification involves milling arrays of perforations directly within the lamella body. These perforations are designed to function as crack-arrest holes, intercepting cracks as they appear and preventing, or at least delaying their further propagation. By slowing crack growth, these features increase the likelihood that the lamella remains intact long enough to complete cryo-TEM imaging. The second modification replaces the conventional rigid attachment of the lamella to the surrounding cellular bulk material with a softer suspension using ring-shaped springs formed by ion beam milling. Mounting the lamella on smooth annular springs provides mechanical compliance both across and along the lamella axis, as well as at intermediate angles and in the out-of-plane direction. This flexibility allows the lamella to accommodate larger stresses and deformations without reaching its mechanical failure threshold. We fabricated a series of test lamellae incorporating different crack-arrest hole geometries, as well as lamellae suspended on soft annular springs. We performed high-resolution cryo-TEM imaging to characterise the perforations themselves and characterised the captured crack geometry within the lamellae at the highest level of detail achieved to date. TEM imaging shows crack interception and guided, non-catastrophic failure paths, while simulations confirm lowered stress in suspended lamellae.

molecular biology↗

Mind the corner: Fillets in cryo-FIB lamella preparation to minimise sample loss caused by stress concentration and lamella breakage

Cryo-FIB milling of biological specimens is a critical and limiting step in the cryo-electron tomography workflow. Preparing electron-transparent cryo-lamellae is a serial, low-throughput process. Even with automation, a skilled operator can typically only produce 15-25 lamellae in a single cryo-FIB session. During sample handling, milling and transfer, the cryo-fixed cells as well as the supporting film layer face various mechanical forces and thermal stresses due to temperature fluctuations. Moreover, after cells are cryo-FIB milled, the resulting thin lamellae continue to endure external forces from mechanical handling and thermal stress. We propose a simple, yet highly effective modification to the standard rectangular milling pattern by implementing "fillets" or corner smoothing providing better mechanical stability. This adjustment helps to avoid sharp corners at the lamella edges, thereby reducing stress concentration. As a result, this modification decreases the likelihood of lamella breakage and improves the overall yield of ready-for-TEM lamellae by 33% as verified experimentally.

biochemistry↗

OpenFIBSEM: an application programming interface for easy FIB/SEM automation

Automation in microscopy is the key to success in long and complex experiments. Most microscopy manufacturers provide Application Programming Interfaces (API) to enable communication between a user-defined program and the hardware. Although APIs effectively allow the development of complex routines involving hardware control, the developers need to build the applications from basic commands. Here we present a Software Development Kit (SDK) for easy control of Focussed Ion Beam Scanning Electron Microscopes (FIB/SEM) microscopes. The SDK, which we named OpenFIBSEM consists of a suite of building blocks for easy control that simplify the development of complex automated workflows.

cell biology↗

Oxygen plasma focused ion beam scanning electron microscopy for biological samples

Over the past decade, gallium Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) has been established as a key technology for cellular tomography. The utility of this approach, however, is severely limited both by throughput and the limited selection of compatible sample preparation protocols. Here, we address these limitations and present oxygen plasma FIB (O-PFIB) as a new and versatile tool for cellular FIB-SEM tomography. Oxygen displays superior resin compatibility to other ion beams and produces curtain-free surfaces with minimal polishing. Our novel approach permits more flexible sample preparation and 30% faster data collection when compared to using gallium ion sources. We demonstrate this alternative FIB is applicable to a variety of embedding procedures and biological samples including brain tissue and whole organisms. Finally, we demonstrate the use of O-PFIB to produce targeted FIB-SEM tomograms through fiducial free en-block correlative light and electron microscopy.

cell biology↗