Systems Neuroscience Imaging Resource

National Institute Of Mental Health

Investigators

Linked publications & trials

Abstract

Summary The mission of the NIMH Systems Neuroscience Imaging Resource (SNIR) is to make advanced light microscopy related techniques available to Intramural Program investigators. This is its seventh year of operation. SNIR functions can be divided into three interacting domains: acquisition and maintenance of equipment and software, development and implementation of procedures, and training. The COVID-19 pandemic had a major effect on its operation, but the resource is fully functional. Some processes put in place during the pandemic have been retained and expanded because they make access more convenient as well as safe. This includes the ability to use all image processing workstations and software remotely as well as carrying out most software training remotely. Major supported equipment includes: 1) Zeiss AxioscanZ1 slide scanning microscope (2016 acquisition). This is a high quality widefield microscope with transmitted brightfield and fluorescent epi-illumination capacity. Its most significant feature is the ability to program multichannel tiled acquisition of large areas from up to 100 microscope slides. It is being actively used by investigators from more than 10 intramural laboratories for projects that include whole brain mapping of gene expression profiles and the projections of genetically tagged and fluorescently labeled neuron populations. The system is used to capacity. 2) Zeiss LSM780 microscope (2011 acquisition, now a secondary instrument). This is a high quality inverted confocal microscope with 405, 488, 514, 561, 594 and 633 nm lasers, a 32-channel GaAsP based spectral detector and 2 conventional PMTs. 3) LaVision Ultrascope (2017 acquisition). This is a light sheet microscope optimized for low magnification (1.2 to 12X 0.5 NA objective with a minimum light sheet thickness minimum of 5 microns) imaging of large samples (up to approximately 10 x 10 x 6 mm). It has 405, 488, 552, 638, and 740 nm lasers. Whole mouse brains immunolabeled with the iDISCO technique and cleared with CUBIC, SHIELD and other procedures are being imaged. This system is largely being replaced by an instrument from Intelligent Imaging Innovations (3i). 4) Leica SP8 confocal/multiphoton system (2017 acquisition). This is an upright microscope equipped with standard objectives and long working distance dipping objectives designed for work with thick cleared samples. It is equipped with 405, 488, 552 and 638 nm fixed lasers and an Insight X3 tunable IR laser, and both internal, and external non-descanned, PMT and HyD detectors. It has capacity to perform fluorescent lifetime imaging microscopy (FLIM). 5) Nikon A1HR confocal system (2020 acquisition). This is set up for both widefield epillumination and laser scanning confocal imaging and includes both galvanometer and resonant scanning ability. It is equipped with 405, 488, 561, 630 and 750 nm lasers. 6) Leica Stellaris confocal instrument (2020 acquisition). This is equipped with a tunable pulsed white light laser as well as 5 tunable high sensitivity detectors that support time gated acquisition, providing precise control of excitation wavelength and emission windows from 405 to 8000nm. Image acquisition can be done in galvanometer or resonant modes. 6) Nikon Biopipeline Slide System (2020 acquisition). This is a slide scanning instrument that will provide highly customizable control over acquisition, including imaging of selected regions of interest in either widefield or confocal mode (using confocal components repurposed from a Nikon C2 system). The vendor is working on software implementation. Pilot projects are underway. 7) Intelligent Imaging Innovations (3i)Cleared Tissue Lightsheet Microscope (CTLS) (2022 acquisition). This is an advanced light sheet instrument designed for cleared tissue imaging that uses a spatial light modulator (SLM) to optimize the light sheet shape and long working distance high NA (0.25, 0.35) non-immersion objectives that allow essentially any clearing media to be imaged. It is equipped with 488, 561, 633 and 750 nm lasers. It is replacing the LaVision instrument. Major supported software includes: Microbrightfield Brainmaker and Neurolucida 360. These packages facilitate reconstruction and analysis of the distribution and morphology of labeled neurons. Arivis Vision4D is available for visualization of large - dimensional datasets and implementation of analysis pipelines including segmentation using explicit algorithms and machine learning. In addition, custom python-based code was developed within the group for denoising, deconvolution, dehazing, stitching, segmentation and registration of massive data sets, taking advantage of the NIH Biowulf computational cluster. Training provided this year included: 1) Initial use of each of the microscopes and the software packages described above. 2) Ad hoc assistance during microscope and software use. 3) Use of iDISCO based labeling and clearing for whole mouse brain mapping of immediate early gene distribution. 4) Use of a custom pipeline for atlas registration and whole brain analysis of cells with immediate early gene activation. 5)Whole brain imaging using CUBIC and SHIELD for clearing. 6)Multiplex in situ hybridization. 7) Custom pipelines for multiple round in situ hybridization including subtraction of endogenous fluorescent material (lipofuchsin) and registration of material that has been stripped and reprobed. Publications that used images generated on SNIR microscopes include: Schoenfeld TJ, Rhee D, Smith JA, Padmanaban V, Brockett AT, Jacobs H, Cameron HA (in press) Rewarded maze training increases approach behavior in rats through neurogenesis-dependent growth of ventral hippocampus-prelimbic circuits. Biol Psychiatry Glob Open Sci. Bakalar D, Gavrilova O, Jiang SZ, Zhang HY, Roy S, Williams SK, Liu N, Wisser S, Usdin TB, Eiden LE. Constitutive and conditional deletion reveals distinct phenotypes driven by developmental versus neurotransmitter actions of the neuropeptide PACAP. J Neuroendocrinol. 2023 May 2:e13286. doi: 10.1111/jne.13286. Epub ahead of print. PMID: 37309259. Ma, J., du Hoffmann, J., Kindel, M. et al. Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors.Nat Neurosci 24, 14291440 (2021). https://doi.org/10.1038/s41593-021-00912-7 Claire Gao, Chiraag A Gohel, Yan Leng, Jun Ma, David Goldman, Ariel J Levine, Mario A Penzo (2023) Molecular and spatial profiling of the paraventricular nucleus of the thalamus eLife 12:e81818 https://doi.org/10.7554/eLife.81818 Messanvi KF, Berkun K, Perkins A, Chudasama Y. Parallel Pathways Provide Hippocampal Spatial Information to Prefrontal Cortex. J Neurosci. 2023 Jan 4;43(1):68-81. doi: 10.1523/JNEUROSCI.0846-22.2022. Epub 2022 Nov 22. PMID: 36414405; PMCID: PMC9838712. Qi J, Ye C, Naskar S, Incio AR, Lee S. Posteromedial thalamic nucleus activity significantly contributes to perceptual discrimination. PLoS Biol. 2022 Nov 28;20(11):e3001896. PMID: 36441759 Akitake, B., Douglas, H.M., LaFosse, P.K., Beiran, M., Deveau, C.E., ORawe, J., Li, A.J., Ryan, L.N., Duffy, S.P., Zhou, Z., et al. (2023). Amplified cortical neural responses as animals learn to use novel activity patterns. Current Biology 33, 2163-2174.e4. 10.1016/j.cub.2023.04.032.