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3 Publications

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    Svoboda LabSaalfeld LabSternson LabTillberg Lab
    12/01/21 | EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.
    Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL, Schmidt U, Yang H, Svoboda K, Myers EW, Saalfeld S, Korff W, Sternson SM, Tillberg PW
    Cell. 2021 Dec 01;184(26):6361. doi: 10.1016/j.cell.2021.11.024

    Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

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    05/28/21 | Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy.
    Tillberg P
    Methods in Molecular Biology. 2021 May 28;2304:147-156. doi: 10.1007/978-1-0716-1402-0_7

    Expansion microscopy (ExM) is a method to expand biological specimens ~fourfold in each dimension by embedding in a hyper-swellable gel material. The expansion is uniform across observable length scales, enabling imaging of structures previously too small to resolve. ExM is compatible with any microscope and does not require expensive materials or specialized software, offering effectively sub-diffraction-limited imaging capabilities to labs that are not equipped to use traditional super-resolution imaging methods. Expanded specimens are ~99% water, resulting in strongly reduced optical scattering and enabling imaging of sub-diffraction-limited structures throughout specimens up to several hundred microns in (pre-expansion) thickness.

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    03/08/21 | Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization
    Yuhan Wang , Mark Eddison , Greg Fleishman , Martin Weigert , Shengjin Xu , Frederick E. Henry , Tim Wang , Andrew L. Lemire , Uwe Schmidt , Hui Yang , Konrad Rokicki , Cristian Goina , Karel Svoboda , Eugene W. Myers , Stephan Saalfeld , Wyatt Korff , Scott M. Sternson , Paul W. Tillberg
    bioRxiv. 2021 Mar 8:. doi: 10.1101/2021.03.08.434304

    Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 µm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis of scRNA-Seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

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