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The Light Microscopy Facility offers one-on-one technical support, consultation, and training to ensure optimal use of our many advanced capabilities. Please contact us to help identify the best instrumentation for your imaging needs.

Image Scanning Microscopy (Airyscan):

The Airyscan array detector uses multipoint confocal acquisition combined with pixel reassignment and deconvolution to achieve better resolution and sensitivity. Two-fold resolution enhancement in both the lateral and axial dimensions for 2D and 3D acquisitions can be achieved routinely without requiring any specific sample preparation protocol. Super resolution can be maintained at depths beyond 50 µm into a scattering sample in the presence of substantial out-of-focus fluorescence. Higher SNR with gentler excitation makes it an ideal imaging modality for dim samples and live experiments.​ For more information, please see Additional Information.

  • Zeiss LSM 880 with Airyscan is an inverted confocal microscope designed for optimized productivity using a 32-element multi-channel area detector for higher sensitivity and gentle illumination. The Fast Airyscan module enables super resolution imaging at 4x speed and improved SNR.
  • MOSAIC (Multimodal Optical Scope with Adaptive Imaging Correction) is currently under construction. It combines several imaging modalities with camera-based pixel reassignment and adaptive optics.

Spectral Imaging (linear unmixing):

Spectral imaging combined with linear unmixing is a highly useful technique that can be used in combination with other advanced imaging modalities to untangle fluorescence spectral overlap artifacts in cells and tissues labeled with synthetic fluorophores that would be otherwise difficult to separate. The spectral detector (lambda mode) is used to measure fluorescence emission over a broad range of wavelengths. Using reference emission spectra ('fingerprints'), linear unmixing determines the relative contribution of each fluorophore in every pixel of an image. Consequently, separation of up to eight spectrally overlapping dyes as well as uncharacterized autofluorescence is possible while potentially reducing imaging time by acquiring all dyes in parallel and unmixing them post-acquisition.

  • Zeiss LSM 880 with Airyscan is an inverted confocal microscope with a 32-element internal detector. A 'lambda stack' is analyzed with the Zen software using the Linear Unmixing processing tool such that reference spectra are obtained interactively or automatically using "Multi-channel Unmixing" or "Automatic Component Extraction".
  • Zeiss LSM 880 NLO is an upright confocal microscope with a 32-element internal detector and an adjustable 690-1064 nm (Chameleon) laser.

Light Sheet Fluorescence Microscopy (LSFM):

LSFM or Selective Plane Illumination Microscopy (SPIM) allows fast 3D imaging of large volumes. By gently illuminating a thin section (usually a few hundred nanometers to several microns) of the sample at any given time, this method greatly reduces photodamage and stress on a live sample while achieving good optical sectioning capabilities. In contrast to point scanning techniques, LSFM can acquire images at speeds 100-1000 times faster. For more information, please see Additional Information.

  • Zeiss Lightsheet Z.1 is a turn-key instrument for routine high-speed 3D imaging with intermediate axial resolution. It is tailored for zebrafish and drosophila embryos, whole mouse brain, expanded samples, and transparent specimens (up to 5 mm).
  • Custom-built Lattice Light-sheet employs an optical lattice of Bessel beams to generate an ultra-thin lightsheet resulting in superior axial resolution. It is tailored for zebrafish and drosophila embryos, expanded samples, and transparent specimens (up to 4 mm).
  • MOSAIC is currently under construction. It combines several imaging modalities, including lattice light sheet microscopy, with adaptive optics that are vital for visualizing and quantifying complex biological systems with high spatiotemporal resolution.

Live Cell Incubation (time-lapse imaging):

All of the microscopes can automatically capture series of images over time, however, only several are equipped with temperature and CO2 control for live cell imaging. The integration time per image will depend on the imaging modality along with the detector and stages used. As a result, widefield and light sheet microscopes will offer the fastest frame rates such that triggered acquisitions can exceed 50 Hz, while confocal imaging can rarely exceed 2 Hz. Autofocusing and other modules that maintain the distance between the objective and the coverslip improve system stability by minimizing axial focus fluctuations (i.e., drift) in real time.

  • Zeiss LSM 880 with Airyscan is an inverted confocal microscope with a large incubation unit for global CO2 and temperature control along with heated stage inserts. The Definite Focus (DF) module is available.
  • Nikon Eclipse Ti is an inverted widefield microscope with CO2 control using a heated stage insert along with an objective heater. The Perfect Focusing System (PFS) module is available.
  • Zeiss Lightsheet Z.1 is designed for multi-view imaging of large specimens. The top of the chamber is open for gas exchange and to allow introduction of the sample. CO2 and temperature control via a Peltier block at the bottom of the chamber makes it ideal for live samples including zebrafish.
  • Custom-built Lattice Light-sheet is optimized for expansion microscopy but also has a large bath permitting gas exchange and perfusion for live samples. The incubation unit requires at least a day for the temperature to stabilize to 37°C.
  • MOSAIC is currently under construction. It combines several imaging modalities, including lattice light sheet microscopy, with adaptive optics.

High-throughput Imaging (automated acquisitions):

High-throughput imaging is the use of automation equipment using classical techniques from optics, chemistry, biology, or image analysis to permit rapid, highly parallel research. One of the most common technologies employed in microscopy is slide scanning which allows hundreds of slides (e.g., sectioned mouse brain) to be imaged in a single run using a shared set of acquisition settings.

  • TissueGnostics TissueFAXS 200 is a combination widefield and spinning disk confocal microscope operated as a whole slide digital scanner; optical sectioning from the latter imaging modality offers increased contrast based on rejection of out-of-focus light. Faster acquisitions are possible by only imaging the tissue sections ("automated" detection).
  • 3DHISTECH Pannoramic 250 Flash is a widefield microscope operated as a whole slide digital scanner.

High Content Imaging (automated acquisitions):

Custom acquisitions of sample carriers and multi-well plates can be automated without the need for advanced macros or scripting. Based on real-time image analysis and feedback, acquisitions settings can be programmatically modified on-the-fly.

  • Nikon Eclipse Ti is an inverted widefield microscope that accommodates a range of sample carriers and multi-well plates. The JOBS module can be tailored for advanced acquisitions while also making use of High Content Analysis software with heat maps representation to automatically quantify data on-the-fly.

Advanced Image Processing - Deconvolution:

Deconvolution is an image processing technique used to improve the contrast and resolution of images captured using an optical microscope. Out-of-focus light causes blur in a digital image. Mathematically, this can be represented as a convolution operation. Deconvolution seeks to remove or reassign this light present in 2D and 3D image acquisitions in order to actually attain the desired optical resolution of the imaging system. Nearly all fluoresence images can and should be deconvolved, with advanced techniques like confocal and super resolution microscopy also realizing its benefits. Note that if a system is already diffraction-limited then deconvolution, alone, will not improve resolution nor if sampling is greater than the Nyquist limit. For more information, please see Supplementary Microscope Objectives.

  • Zen is the control and processing software for Zeiss microscopes. Data acquired on these microscopes can be deconvolved using an estimated or experimentally-measured PSF. All imaging modalities are supported.
  • Imaris is visualization and analysis software capable of interactive 3D/4D rendering for large, multi-channel datasets (for most image formats), acquired with any microscope. Light sheet templates and the ability to use an experimentally-measured PSF are lacking.
  • FIJI is an extended distribution of ImageJ with many bundled 3rd party plugins, such as DeconvolutionLab2​. As an open-source alternative, it is robust with multiple algorithms available although it is computationally intensive.
  • Image Processing Pipeline (IPP) offers advanced workflows for light sheet acquisitions. Single volume or tiled acquisitions can be deconvolved quickly on Janelia's compute cluster using an experimentally-measured PSF.

Advanced Image Processing - Big Data Stitching/Fusion:

For tiled acquisitions on light sheet microscopes, it is necessary to align and fuse all tiles/views. The size of typical datasets can range up to several TB; consequently, only certain applications are capable of properly handling 'big data' in an accurate and timely manner.

  • Imaris Stitcher is a stand-alone application for aligning and fusing microscopy image tiles. Individual z-stacks will be shifted with respect to one another to ensure best results; however, the amount of overlap between tiles and the available computer memory will ultimately determine alignment precision. It is ideal for mouse brain and low-resolution acquisitions.
  • FIJI is an extended distribution of ImageJ with many bundled 3rd party plugins, such as BigStitcher. As an open-source alternative, it offers simple and efficient alignment of multi-tile and multi-angle image datasets although it is computationally intensive.
  • IPP offers advanced workflows for light sheet acquisitions by providing a web interface to easily process (on Janelia's compute cluster) and export data in a user-friendly format. Only those modules desired need to be selected including:
    • Flatfield Correction: This procedure compensates for illumination inhomogeneity in the FOV (intensity drop off at edges); a reference image is back calculated from the data itself, thus acquiring more images should yield better results.
    • Deconvolution: It may be necessary to perform deconvolution (deblurring) to achieve the resolution capable for the microscope in addition to improved contrast. A Richardson-Lucy iterative scheme is used with an experimentally-measured PSF such that the number of iterations (strength) can be specified.
    • Stitching: The algorithm applies affine transformations that also grows/shrinks neighboring tiles for better alignment. The size of the dataset should not limit performance.

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