Systems Neuroscience Imaging Resource

系统神经科学成像资源

• 批准号: 10266656
• 负责人: Theodore Usdin
• 金额: $ 287.72万
• 依托单位: NATIONAL INSTITUTE OF MENTAL HEALTH
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10266656
• 关键词: 3-Dimensional; Anatomy; Anosmia; Antibodies; Area; Atlases; Brain; Brain Mapping; Brain region; COVID-19; COVID-19 pandemic; Callithrix; Collaborations; Computer software; Custom; Data; Data Set; Degenerative Disorder; Development; Dimensions; Equipment; Expression Profiling; Functional Imaging; Gene Expression; Genetic; High Prevalence; Histologic; Hour; Human; Image; Image Analysis; Immediate-Early Genes; In Situ Hybridization; Intramural Research Program; Investigation; Label; Laboratories; Laser Scanning Confocal Microscopy; Lasers; Light; Lighting; Macaca; Maintenance; Messenger RNA; Methods; Microscope; Microscopy; Microtome - medical device; Mission; Molecular; Morphology; Mus; National Institute of Biomedical Imaging and Bioengineering; National Institute of Mental Health; National Institute of Neurological Disorders and Stroke; Nature; Neurons; Neurosciences; Nucleic Acid Probes; Pathology; Pattern; Phase; Population; Preparation; Procedures; Proteins; Publications; Ramp; Reaction; Research Personnel; Research Project Grants; Resolution; Resources; Sampling; Scanning; Slide; Specific qualifier value; Structure; System; Techniques; Technology; Thick; Time; Tissue imaging; Tissues; Training; Training Support; Visualization; Work; analysis pipeline; base; cell type; confocal imaging; cryostat; denoising; design; detector; image processing; imaging capabilities; insight; instrument; interest; light microscopy; microscopic imaging; millimeter; molecular imaging; neuroinflammation; olfactory bulb; operation; programs; protein distribution; reconstruction; routine imaging; software development; student training; tissue preparation; tool

Summary The NIMH Systems Neuroscience Imaging Resource (SNIR) mission is to make advanced light microscopy related techniques available to Intramural Program investigators. This is its fourth 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. 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 have been established. 2) Zeiss LSM780 microscope (2011 acquisition). 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. Prior to COVID-19 it was used to capacity during core working hours by investigators from approximately 10 different NIMH intramural groups. It is returning to operation with the phased return to campus. 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 10 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 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 C2 system (2016 acquisition). This is set up for both widefield epillumination and laser scanning confocal imaging. The microscope provides alternatives to the Zeiss Axioscan and LSM780 that are being used to capacity. It also provides the unique capacity to scan large areas in widefield mode at low or moderate magnification and to subsequently image regions of interest at high resolution and/or in confocal mode. 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. 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 hairpin chain reaction based in situ hybridization. 4) 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. This year a new collaboration with the Advanced Imaging and Microscopy facility in NIBIB (AIM) was established. In this collaboration a dual inverted Selected Plane Illumination Microscope (diSPIM) optimized for imaging cleared tissue will be built and maintained by AIM. Together we plan to develop procedures for high resolution, isomorphic, imaging of whole brains. The microscope was assembled and established to be functional for imaging cleared tissue slabs up to a millimeter thick. Planned implementation of real-time sectioning and image processing procedures were put on hold when campus activities were reduced. Work on this project has resumed. A new experimental direction was established to contribute to the understanding of COVID-19 pathology. There is a high prevalence of anosmia associated with COVID-19, with an unknown basis. We have an ongoing collaboration with the NINDS Koretsky laboratory to investigate structural changes in the human olfactory bulb associated with degenerative diseases. We plan to extend this to examine effects of COVID-19 on the olfactory bulb, taking advantage of the SNIR 3-dimensional tissue imaging capability. Publications that used images generated on SNIR microscopes include: 1. Gao C. .. Penzo MA. 2020. Nature Neuroscience, 23(2), 217228. PMID: 31932767 2. Williams Avram S .. Young WS. 2019. Front Behav Neurosci. 13. PMID: 31787886 3. Young WS, Song J. 2020 Front Mol Neurosci. 13. PMID: 32256314 4. Cymerblit-Sabba A .. Young WS. 2020. bioRxiv. doi: 10.1101/2020.05.11.078915. 5. Sanzeni A. Histed MH. Elife. 2020 29;9. PMID: 32598278 6. Nordman J .. Li Z. eNeuro. 2020 Jul 23;7(4) PMID: 32651265 7. Shen H .. Li Z. Nat Commun. 2020 Jun 12;11(1):2979. PMID: 32532981 8. Nordman JC .. Li Z. J Neurosci. 2020 Jun 17;40(25):4858-4880. PMID: 32424020 9. Shrestha S .. Innis RB. 2020. J Neuroinflammation 17(1): 140. PMID: 32359360 10. Lehmann MLM ... .. Herkenham M. 2020. Brain Behav Immun 88: 735-747. PMID: 32413560

概括 NIMH系统神经科学成像资源（SNIR）任务是使高级光学显微镜与壁内计划研究人员相关的技术。这是其运营的第四年。 SNIR功能可以分为三个相互作用的域：设备和软件的获取和维护，程序的开发和实施以及培训。 COVID-19大流行对其运作产生了重大影响，但许多活动仍在继续。尤其是通过远程访问提供图像处理资源。 主要支持的设备包括：1）Zeiss Axioscanz1幻灯片扫描显微镜（2016年收购）。这是一个高质量的广场显微镜，具有传播的Brightfield和荧光表演能力。它最重要的功能是能够编程多通道瓷砖从最高100个显微镜幻灯片进行大面积采集。来自10个不同壁内实验室的研究人员正在积极使用它，用于包括基因表达谱的整个大脑映射以及遗传标记和荧光标记神经元种群的投影。该系统用于容量，直到由于19号而降低了校园入住率。随着分阶段返回校园，使用迅速增加。已经建立了与处理与乐器进行物理互动的技术人员进行远程互动的程序。 2）Zeiss LSM780显微镜（2011年收购）。这是具有405、488、514、561、594和633 nm激光器，一个基于32频道GAASP的光谱检测器和2个常规PMT的高质量倒置共聚焦显微镜和633 nm激光器。在COVID-19之前，它在核心工作时间内使用了大约10个不同NIMH室内组的研究人员的能力。随着分阶段返回校园，它正在恢复运营。 3）Lavision Ulterscope（2017年收购）。这是用于优化低放大倍率的轻型显微镜（1.2至12x 0.5 Na物镜，最小的轻度厚度最小厚度为10微米）的大型样品成像（大约10 x 10 x 6 mm）。它具有405、488、552、638和740 nm激光器。用IDISCO技术进行的全鼠免疫标记的整个大脑正在定期成像，并且使用Cubic和其他程序清除的大脑的项目正在开发中。 4）Leica SP8共聚焦/多光系统（2017年收购）。这是一个直立的显微镜，配备了较长的工作距离浸入目标，该目标是为厚实的样品工作而设计的。它配备了405、488、552和638 nm固定激光器和洞察力X3可调IR激光，以及内部和外部非偏见，PMT和HYD探测器。它具有执行荧光寿命成像显微镜（FLIM）的能力。 5）尼康C2系统（2016年收购）。这是针对广场癫痫发光和激光扫描共聚焦成像而设置的。显微镜为用于容量的Zeiss Axioscan和LSM780提供了替代方案。它还提供了独特的能力，可以在低或中等放大倍率下以宽阔的模式扫描大面积，然后在高分辨率和/或共聚焦模式下图像感兴趣的区域。 主要支持的软件包括：Microbrightfield Brainmaker和Neurolucida 360。这些软件包有助于重建和分析标记神经元的分布和形态。 Arivis Vision4D可用于可视化大维数据集和分析管道的实现。 今年提供的培训包括：1）最初使用每个显微镜以及上述软件包。 2）在显微镜和软件使用过程中进行临时帮助。 3）使用基于原位杂交的发夹链反应。 4）使用基于IDISCO的清除量来进行全小鼠脑映射，以立即的早期基因分布。 5）使用自定义管道进行地图集注册和标记的整个小鼠脑数据的神经元分割。 今年建立了与尼比布（AIM）的高级成像和显微镜设施的新合作。在这种合作中，将通过AIM构建和维护用于成像清除组织成像的双重选择平面照明显微镜（DESPIM）。我们计划共同开发用于高分辨率，同构，整个大脑成像的程序。将显微镜组装成并确定，可用于成像清除的组织板，直至毫米厚。减少校园活动时，计划实施实时分段和图像处理程序。该项目的工作已经恢复。 建立了一个新的实验方向，以有助于对Covid-19病理的理解。与COVID-19相关的厌氧血症患病率很高，基于未知。我们与Ninds Koretsky实验室进行了持续的合作，以研究与退行性疾病相关的人类嗅球的结构变化。我们计划扩展这一点，以利用SNIR 3维组织成像能力来检查Covid-19对嗅球的影响。 使用SNIR显微镜上生成的图像的出版物包括： 1。GaoC. .. Penzo MA。 2020年。自然神经科学，23（2），217228。PMID：31932767 2。WilliamsAvram S .. Young Ws。 2019年。前部行为神经科学。 13。PMID：31787886 3。Young WS，Song J. 2020前Mol Neurosci。 13。PMID：32256314 4。cymerblit-sabba a .. Young Ws。 2020。Biorxiv。 doi：10.1101/2020.05.11.078915。 5。SanzeniA.历史记录。 Elife。 2020 29; 9。 PMID：32598278 6。NordmanJ .. Li Z. Eneuro。 2020年7月23日； 7（4）PMID：32651265 7。ShenH .. Li Z. Nat Commun。 2020年6月12日； 11（1）：2979。 PMID：32532981 8。NordmanJC .. Li Z. J Neurosci。 2020年6月17日； 40（25）：4858-4880。 PMID：32424020 9。Shresthas .. Innis RB。 2020。J神经炎症17（1）：140。PMID：32359360 10。LEHMANNMLM ... .. HERKENHAM M.2020。脑行为免疫88：735-747。 PMID：32413560