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 sixth 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. Image processing resources, in particular, are available through remote access. Procedures have been put in place for safe training and 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 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 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. 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. 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, dehazing, 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- and SHIELD based 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. Publications that used images generated on SNIR microscopes include: 1. Helseth AR, Hernandez-Martinez R, Hall VL, Oliver ML, Turner BD, Caffall ZF, Rittiner JE, Shipman MK, King CS, Gradinaru V, Gerfen C, Costa-Mattioli M, Calakos N (2021) Cholinergic neurons constitutively engage the ISR for dopamine modulation and skill learning in mice Science. 372 eabe1931. PMID: 33888613 2. Naskar, S., Qi, J., Gerfen, C.R., and Lee, S. (2021). Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs. Cell Reports 34(8): 108774. PMID: 33626343 3. Inagaki HK, Chen S, Ridder MC, Sah P, Li N, Yang Z, Hasanbegovic H, Gao Z, Gerfen CR, Svoboda K. A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement. Cell. 2022 Mar 17;185(6):1065-1081.e23. doi: 10.1016/j.cell.2022.02.006. Epub 2022 Mar 3. PMID: 35245431; PMCID: PMC8990337. 4. Qi J, Ye C, Naskar S, Inacio AR, Lee S. The role of a higher-order thalamic nucleus in perceptual discrimination. (Under revision, PLOS Biology, PBIOLOGY-D-21-03329R1) 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. 5. Ma J, du Hoffmann J, Kindel M, Beas BS, Chudasama Y, Penzo MA. Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors. Nat Neurosci. 2021 Oct;24(10):1429-1440. doi: 10.1038/s41593-021-00912-7. Epub 2021 Aug 19. PMID: 34413514; PMCID: PMC8484052.