Software Description
This open-source executable code is for post-acquisition deconvolution of data produced by the lattice light-sheet microscope developed by Eric Betzig's group at HHMI's Janelia Research Campus. It can also deskew data acquired in the sample scan mode. Sample data and usage examples are provided. The software incorporates unmodified libraries from a variety of sources, packaged together for easy implementation.
Opportunity
The Tip-Tilt-Z Sample Positioner provides automated rotation of a head-fixed rodent specimen about the anterior-posterior and mediolateral axes for imaging or other purposes. The device also provides automated Z translation and can be customized to accommodate various head bar designs.
Rotation range, each axis: +/-10 deg
Z travel varies depending on the angular orientation of the sample:
minimum Z travel: +/- 8.5 mm
maximum Z travel: +/- 25mm
Researchers at Janelia have designed an improved head plate for live imaging of a mouse using a downward-facing objective. It is specially designed to work with the 2P-RAM (2-photon random access mesoscope).
The Janelia PMT Controller is an updated design for use in high-performance microscopy systems. It was designed and built to meet the needs of the new large field of view 2 photon random access mesoscope, also available via license or purchase. You can find the complementary PMT Amplifier here.
Hardware Overview
Researchers at HHMI Janelia Research Campus have designed and built a 2-photon random access mesoscope (2P-RAM) that provides rapid imaging anywhere within a large tissue volume.
Cellular imaging can link activity in populations of neurons with behavior. But individual neurons are small, around 10μm in diameter. Most microscopes with subcellular resolution have small fields of view and, therefore, cannot image neurons in multiple brain areas simultaneously. Most large-field-of-view microscopes do not resolve single cells, especially in the axial dimension.
The Low Voltage Differential Signaling (LVDS) cable driver provides a fast, low noise transmission of a TTL up signal to a remote location while providing some protection against ground differences.
MicroED is a recently developed method from the Gonen lab, which allows collecting high-resolution electron diffraction data from tiny protein microcrystals using an electron cryo-microscope (cryo-EM).
For MicroED, the standard transmission electron microscopy (TEM) equipment is used with one modification: a constant rotation-controlling device, the MicroED Stage Controller.
Genomic DNA in cells is highly folded and organized in three dimensions. Detection and visualization of genomic DNA are widely accomplished by using various fluorescence in situ hybridization (FISH) methods. However, despite enhancements to DNA FISH methods, the use of chemicals or heat in the process results in denaturation of the DNA and potentially affects the integrity of the biological structure, which limits research related to the understanding of gene expression.
The standard reflection objective is designed to work in air with reasonably high resolution. It is a lightweight, simple structure (only one or two mirrors are needed) with little chromatic dispersion and a relatively long working distance. However, it cannot be used in an immersion medium other than air. Otherwise, the light passing through the objective will suffer from considerable aberrations, and those will reduce resolution at the sample.
The Janelia Fluor® dyes are a next-generation small-molecule fluorophore platform that combines superior brightness, photostability, and cell permeability with unprecedented modularity, allowing fine-tuning of spectral and chemical properties for specific biological applications. Developed using novel azetidine substitution of rhodamine dyes, these fluorophores can be optimized for different biological imaging experiments ranging from super-resolution microscopy to in vivo imaging.
