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 fifth 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 many activities continued. Image processing resources, in particular, were made available through remote access. With partial return to the workplace, procedures were put in place for safe use of equipment. Essentially all requests for use of equipment were accommodated. 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 10 different 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 was used to capacity until campus occupancy was reduced because of COVID-19. Use ramped up quickly with the phased return to campus. Procedures for remote interactions with a technician who handles physical interactions with the instrument were established. 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 are being imaged routinely and projects using brains cleared with CUBIC, SHIELD and other procedures are under development. 4) Leica SP8 confocal/multiphoton system (2017 acquisition). This is an upright microscope equipped with 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, providing precise control of excitation wavelength and emission windows from 405 to 730nm. Scanning 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. The system is not yet available to users. 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. In addition custom python-based code was developed within the group for denoising, deconvolution, stitching, and segmentation 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 clearing for whole mouse brain mapping of immediate early gene distribution. 5) Use of a custom pipeline for atlas registration and labeled neuron segmentation of whole mouse brain data. Publications that used images generated on SNIR microscopes include: 1. Panja D, Li Y, Ward M, Li Z. miR-936 is increased in schizophrenia and inhibits neural development and AMPA receptor-mediated synaptic transmission. Schizophrenia Bulletin 2021 May 3. 2. Nordman J and Li Z. The Dorsal Raphe Regulates the Duration of Attack through the Medial Orbitofrontal Cortex and Medial Amygdala. eNeuro. 2020 Oct 26;7(5). 3. Nordman J, Ma X, Li Z. Traumatic Stress Induces Prolonged Aggression Increase through Synaptic Potentiation in the Medial Amygdala Circuits. eNeuro. 2020 Jul 23;7(4). 4. Shen H, Zhu H, Panja D, Gu Q, Li Z. Autophagy controls the induction and developmental decline of NMDAR-LTD through endocytic recycling. Nature Commun. 2020 Jun 12;11(1):2979. 5. Nordman J, Ma X, Gu Q, Potegal M, Li H, Kravitz A, Li. Z. Potentiation of divergent medial amygdala pathways drives experience-dependent aggression escalation. J Neurosci. 2020 Jun 17;40(25):4858-4880. 6. Petrus E, Dembling S, Usdin T, Isaac JTR, Koretsky AP. Circuit-Specific Plasticity of Callosal Inputs Underlies Cortical Takeover. J Neurosci. 2020 Sep 30;40(40):7714-7723. doi: 10.1523/JNEUROSCI.1056-20.2020. Epub 2020 Sep 10. PMID: 32913109; PMCID: PMC7531555. 7. Naskar S, Qi J, Pereira F, Gerfen CR, Lee S. Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs. Cell Rep. 2021 Feb 23;34(8):108774. doi: 10.1016/j.celrep.2021.108774. PMID: 33626343; PMCID: PMC7995594. 8. Jun Ma, Johann du Hoffmann, Morgan Kindel, B. Sofia Beas, Yogita Chudasama, Mario A. Penzo. (accepted) Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors. Nature Neuroscience. 9. B. Sofia Beas, Xinglong Gu, Yan Leng, Omar Koita, Shakira Rodriguez-Gonzalez, Morgan Kindel, Bridget A. Matikainen-Ankney, Rylan S. Larsen, Alexxai V. Kravitz, Mark A. Hoon, Mario A. Penzo. (2020) A ventrolateral medulla-midline thalamic circuit for hypoglycemic feeding. Nature Communications, Article number: 6218. 10. Lehmann ML, Poffenberger CN, Elkahloun AG, Herkenham M. Analysis of cerebrovascular dysfunction caused by chronic social defeat in mice. Brain Behav Immun. 2020 Aug;88:735-747. doi: 10.1016/j.bbi.2020.05.030. Epub 2020 May 12. PMID: 32413560; PMCID: PMC7416466. 11. Elliott AD, Berndt A, Houpert M, Roy S, Scott RL, Chow CC, Shroff H, White BH. Pupal behavior emerges from unstructured muscle activity in response to neuromodulation in Drosophila. Elife. 2021 Jul 8;10:e68656. doi: 10.7554/eLife.68656. PMID: 34236312; PMCID: PMC8331185