Time to Upgrade: A New OpenSPIM Guide to Build and Operate Advanced OpenSPIM Configurations – Girstmair – – Advanced Biology – Wiley Online Library

Abstract:  OpenSPIM is an Open Access platform for Selective Plane Illumination Microscopy (SPIM) and allows hundreds of laboratories around the world to generate and process light-sheet data in a cost-effective way due to open-source hardware and software. While setting up a basic OpenSPIM configuration can be achieved expeditiously, correctly assembling and operating more complex OpenSPIM configurations can be challenging for routine standard OpenSPIM users. Detailed instructions on how to equip an OpenSPIM with two illumination sides and two detection axes (X-OpenSPIM) are provided, and a solution is also provided on how the temperature can be controlled in the sample chamber. Additionally, it is demonstrated how to operate it by implementing an ArduinoUNO microcontroller and introducing ?OpenSPIM, a new software plugin for OpenSPIM, to facilitate image acquisition. The new software works on any OpenSPIM configuration comes with drift correction functionality, on-the-fly image processing, and gives users more options in the way time-lapse movies are initially set up and saved. Step-by-step guides are also provided within the Supporting Information and on the website on how to align the lasers, configure the hardware, and acquire images using ?OpenSPIM. With this, current OpenSPIM users are empowered in various ways, and newcomers striving to use more advanced OpenSPIM systems are helped.


An open-access volume electron microscopy atlas of whole cells and tissues | Nature

Abstract:  Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels1. Owing to advances in the precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle2) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and pose questions.