Webinars and Online Tutorials

  • Policies

    1. Training requirement: You only have access to equipment you have been trained on by a member of the MicRoN staff and currently have access to in your PMS account.

    2. Acknowledgement agreement: The MicRoN is supported by Harvard University through a TnT grant. To help us with grant renewal, we ask users to please acknowledge the "Microscopy Resources on the North Quad (MicRoN) core at Harvard Medical School" in any publications or public presentations that contain data acquired or analyzed in the MicRoN core.

    3. Record microscopy usage: You must log onto and sign out any MicRoN microscope computers using your PPMS credentials.

    4. Booking and using the microscopes: Please, do not let another person use the time you have book under your name. Cancel your remaining session and ask other users to book the microscope. Please, never share your eCommons/PPMS credentials with other users.

    5. MicRoN users are not authorized to train or allow others to use a microscope in the MicRoN core. Please, do not allow anyone to use the microscopes if they haven’t been trained by the MicRoN staff.

    6. Reservation limitations: The reservation limitations for each microscope are described at the top of the microscope's PPMS online scheduling page. If you are in dire need for more time, please contact the MicRoN manager (paula_monterollopis@hms.harvard.edu).

    7. Cancellation Policy: You must cancel your session as soon as you know you don't need it. Cancelling less than 24h in advance results in the charge of 50% of the fee, unless the session is booked by another user. No-show sessions result in billing 100% of the fee.  

    8. Report problems: Please if you notice that a microscope is not working appropriately or if you are not sure how to use the equipment, please report it to the MicRoN staff. If you break a slide/coverslip/dish, or drip a liquid/solution onto any part of the imaging system, or in any other way may have caused damage, you must report the problem immediately. You will not be in trouble if you report an issue/possible damage, only if you fail to do so.

    9. Please, do not change the equipment: Do not remove objectives, filter cubes, or any microscope part you are not authorized to. Same for installing software, or reconfiguring settings in the acquisition software.

    10. Data Managment: Please note, microscope computers are not long-term data storage devices. Please back up your data into your server/hard-drive as soon as possible.

  • Publications supported by MicRoN

    Publications supported by MicRoN since 2018 (non-comprehensive!)

    (bold and *** collaborations with researchers)

        1.Fenton, A. K. et al. Phosphorylation-dependent activation of the cell wall synthase PBP2a in Streptococcus pneumoniae by MacP. Proceedings of the National Academy of Sciences of the United States of America 115, 2812–2817 (2018).

        2.Kamareddine, L. et al. Activation of Vibrio cholerae quorum sensing promotes survival of an arthropod host. Nature Microbiology 3, 243–252 (2018).

        3.Xu, C. et al. The Septate Junction Protein Tsp2A Restricts Intestinal Stem Cell Activity via Endocytic Regulation of aPKC and Hippo Signaling. Cell Rep 26, 670–688 (2019).

        4.Wang, S. K., Xue, Y., Rana, P., Hong, C. M. & Cepko, C. L. Soluble CX3CL1 gene therapy improves cone survival and function in mouse models of retinitis pigmentosa. Proc Natl Acad Sci U S A 116, 10140–10149 (2019).

        5.Spallanzani, R. G. et al. Distinct immunocyte-promoting and adipocyte-generating stromal components coordinate adipose tissue immune and metabolic tenors. Sci Immunol 4, (2019).

        6.Kishi, J. Y. et al. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods 16, 533–544 (2019).

        7.He, L., Binari, R., Huang, J., Falo-Sanjuan, J. & Perrimon, N. In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer. Elife 8, (2019).

        8.Lim, H. C. et al. Identification of new components of the RipC-FtsEX cell separation pathway of Corynebacterineae. PLoS Genet 15, e1008284 (2019).

        9.Brunet, Y. R., Wang, X. & Rudner, D. Z. SweC and SweD are essential co-factors of the FtsEX-CwlO cell wall hydrolase complex in Bacillus subtilis. PLoS Genet 15, e1008296 (2019).

        10.Huycke, T. R. et al. Genetic and Mechanical Regulation of Intestinal Smooth Muscle Development. Cell 179, 90–105 (2019).

        11.Lim, H. C. & Bernhardt, T. G. A PopZ-linked apical recruitment assay for studying protein-protein interactions in the bacterial cell envelope. Mol Microbiol 112, 1757–1768 (2019).

        12.Atsuta, Y., Tomizawa, R. R., Levin, M. & Tabin, C. J. 1.2 regulates chondrogenesis during limb development. Proc Natl Acad Sci U S A 116, 21592–21601 (2019).

        13.Taguchi, A. et al. FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein. Nature Microbiology 4, 587–594 (2019).

        14.Atsuta, Y., Tomizawa, R. R., Levin, M. & Tabin, C. J. L-type voltage-gated Ca2+ channel CaV1.2 regulates chondrogenesis during limb development. Proceedings of the National Academy of Sciences of the United States of America 116, 21592–21601 (2019).

        15.Kwon, Y. v. et al. The role of translationally controlled tumor protein in proliferation of Drosophila intestinal stem cells. Proceedings of the National Academy of Sciences of the United States of America 116, 26591–26598 (2019).

        16.Dobihal, G. S., Brunet, Y. R., Flores-Kim, J. & Rudner, D. Z. Homeostatic control of cell wall hydrolysis by the WalRK two-component signaling pathway in Bacillus subtilis. eLife 8, (2019).

        17.Zullo, J. M. et al. Regulation of lifespan by neural excitation and REST. Nature 574, 359–364 (2019).

        18.Xiong, W. et al. AAV cis-regulatory sequences are correlated with ocular toxicity. Proceedings of the National Academy of Sciences of the United States of America 116, 5785–5794 (2019).

        19.Song, W. et al. Tumor-Derived Ligands Trigger Tumor Growth and Host Wasting via Differential MEK Activation. Developmental Cell 48, 277-286.e6 (2019).

        20.György, B. et al. Gene Transfer with AAV9-PHP.B Rescues Hearing in a Mouse Model of Usher Syndrome 3A and Transduces Hair Cells in a Non-human Primate. Molecular Therapy - Methods and Clinical Development 13, 1–13 (2019).

        21.Amamoto, R. et al. Probe-seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation. eLife 8, (2019).

        22.Nerurkar, N. L., Lee, C. H., Mahadevan, L. & Tabin, C. J. Molecular control of macroscopic forces drives formation of the vertebrate hindgut. Nature 565, 480–484 (2019).

        23.Fields, B. D., Nguyen, S. C., Nir, G. & Kennedy, S. A multiplexed dna fish strategy for assessing genome architecture in caenorhabditis elegans. eLife 8, (2019).

        24.Tuncel, J., Benoist, C. & Mathis, D. T cell anergy in perinatal mice is promoted by T reg cells and prevented by IL-33. Journal of Experimental Medicine 216, 1328–1344 (2019).

        25.Amamoto, R. et al. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic Acids Res 48, e4 (2020).

        26.Fivenson, E. M. & Bernhardt, T. G. An Essential Membrane Protein Modulates the Proteolysis of LpxC to Control Lipopolysaccharide Synthesis in Escherichia coli. mBio 11, (2020).

        27.Chen, J. W. et al. The mevalonate pathway is a crucial regulator of tendon cell specification. Development 147, (2020).

        28.Ewen-Campen, B., Comyn, T., Vogt, E. & Perrimon, N. No Evidence that Wnt Ligands Are Required for Planar Cell Polarity in Drosophila. Cell Rep 32, 108121 (2020).

        29.Marmont, L. S. & Bernhardt, T. G. A conserved subcomplex within the bacterial cytokinetic ring activates cell wall synthesis by the FtsW-FtsI synthase. Proc Natl Acad Sci U S A 117, 23879–23885 (2020).

        30.pez-Rivera, F. et al. Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences. G3 (Bethesda) 10, 4473–4482 (2020).

        31.Ghosh, A. C. et al. PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity. Elife 9, (2020).

        32.Lyon, K. A. et al. Sex-Specific Role for Dopamine Receptor D2 in Dorsal Raphe Serotonergic Neuron Modulation of Defensive Acoustic Startle and Dominance Behavior. eNeuro 7, (2020).

        33.Sjodt, M. et al. Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex. Nature Microbiology 5, 813–820 (2020).

        34.Wang, S. K., Lapan, S. W., Hong, C. M., Krause, T. B. & Cepko, C. L. In Situ Detection of Adeno-associated Viral Vector Genomes with SABER-FISH. Molecular Therapy - Methods and Clinical Development 19, 376–386 (2020).

        35.Chan, C. S. Y. et al. Cell type- And stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina. Development (Cambridge) 147, (2020).

        36.Kim, K. et al. Drosophila as a model for studying cystic fibrosis pathophysiology of the gastrointestinal system. Proceedings of the National Academy of Sciences of the United States of America 117, 10357–10367 (2020).

        37.Ingaramo, M. C., Sánchez, J. A., Perrimon, N. & Dekanty, A. Fat Body p53 Regulates Systemic Insulin Signaling and Autophagy under Nutrient Stress via Drosophila Upd2 Repression. Cell Reports 33, (2020).

        38.Sher, J. W., Lim, H. C. & Bernhardt, T. G. Global phenotypic profiling identifies a conserved actinobacterial cofactor for a bifunctional pbp-type cell wall synthase. eLife 9, (2020).

        39.Wang, S. K., Xue, Y. & Cepko, C. L. Microglia modulation by TGF-β1 protects cones in mouse models of retinal degeneration. Journal of Clinical Investigation 140, 4360–4369 (2020).

        40.Perez-Cervantes, C. et al. Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development (Cambridge) 147, (2020).

        41.Yakhnina, A. A. & Bernhardt, T. G. The Tol-Pal system is required for peptidoglycan-cleaving enzymes to complete bacterial cell division. Proceedings of the National Academy of Sciences of the United States of America 117, 6777–6783 (2020).

        42.Amon, J. D. et al. SwsB and SafA are required for CwlJ-dependent spore germination in bacillus subtilis. Journal of Bacteriology 202, (2020).

        43.Truong, T. T., Vettiger, A. & Bernhardt, T. G. Cell division is antagonized by the activity of peptidoglycan endopeptidases that promote cell elongation. Molecular Microbiology 114, 966–978 (2020).

        44.Xu, C. et al. An in vivo RNAi screen uncovers the role of AdoR signaling and adenosine deaminase in controlling intestinal stem cell activity. Proceedings of the National Academy of Sciences of the United States of America 117, 464–471 (2020).

        45.Hung, R. J. et al. A cell atlas of the adult Drosophila midgut. Proceedings of the National Academy of Sciences of the United States of America 117, 1514–1523 (2020).

        46.Ivanchenko, M. v. et al. Preclinical testing of AAV9-PHP.B for transgene expression in the non-human primate cochlea. Hearing Research 394, (2020).

        47.Ghosh, A. C. et al. Drosophila pdgf/vegf signaling from muscles to hepatocyte-like cells protects against obesity. eLife 9, 1–61 (2020).

        48.Okaty, B. W. et al. A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons. eLife 9, 1–44 (2020).

        49.Michowski, W. et al. Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Molecular Cell 78, 459-476.e13 (2020).

        50.Wang, K. et al. Neuronal, stromal, and T-regulatory cell crosstalk in murine skeletal muscle. Proceedings of the National Academy of Sciences of the United States of America 117, 5402–5408 (2020).

        51.López-Rivera, F. et al. A mutation in the drosophila melanogaster eve stripe 2 minimal enhancer is buffered by flanking sequences. G3: Genes, Genomes, Genetics 10, 4473–4482 (2020).

        52.Lai, N. Y. et al. Gut-Innervating Nociceptor Neurons Regulate Peyer’s Patch Microfold Cells and SFB Levels to Mediate Salmonella Host Defense. Cell 180, 33-49.e22 (2020).

        53.Huang, S. et al. Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential. Cell 184, 441–459 (2021).

        54.Ward, T. et al. Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. Circ Res 128, 1156–1169 (2021).

        55.Parkhitko, A. A. et al. Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. PLoS Genet 17, e1009354 (2021).

        56.Tang, H. W. et al. A RNA methylation to suppress autophagy. Proc Natl Acad Sci U S A 118, (2021).

        57.Ivanchenko, M. v et al. AAV-S: A versatile capsid variant for transduction of mouse and primate inner ear. Mol Ther Methods Clin Dev 21, 382–398 (2021).

        58.Droujinine, I. A. et al. Proteomics of protein trafficking by in vivo tissue-specific labeling. Nat Commun 12, 2382 (2021).

        59.Artzi, L. et al. Dormant spores sense amino acids through the B subunits of their germination receptors. Nat Commun 12, 6842 (2021).

        60.DeLoid, G. M. et al. Toxicity, uptake, and nuclear translocation of ingested micro-nanoplastics in an in vitro model of the small intestinal epithelium. Food and Chemical Toxicology 158, (2021). ***

        61.Xue, Y. et al. Aav-txnip prolongs cone survival and vision in mouse models of retinitis pigmentosa. eLife 10, (2021).

        62.Grimes, W. N. et al. A high-density narrow-field inhibitory retinal interneuron with direct coupling to Müller glia. Journal of Neuroscience 41, (2021).

        63.Chan, Y. K. et al. Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses. Science Translational Medicine 13, (2021).

        64.Wu, D. M. et al. Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa. JCI Insight 6, (2021).

        65.Tang, H. W. et al. mTORC1-chaperonin CCT signaling regulates m6A RNA methylation to suppress autophagy. Proceedings of the National Academy of Sciences of the United States of America 118, (2021).

        66.Wang, S. K., Xue, Y. & Cepko, C. L. Augmentation of CD47/SIRP α signaling protects cones in genetic models of retinal degeneration. JCI Insight 6, (2021).

        67.Ding, G. et al. Coordination of tumor growth and host wasting by tumor-derived Upd3. Cell Reports 36, (2021).

        68.Bohrhunter, J. L., Rohs, P. D. A., Torres, G., Yunck, R. & Bernhardt, T. G. MltG activity antagonizes cell wall synthesis by both types of peptidoglycan polymerases in Escherichia coli. Molecular Microbiology 115, 1170–1180 (2021).

        69.Liew, P. X. Mired in the glomeruli: witnessing live neutrophil recruitment in the kidney. American Journal of Physiology - Cell Physiology 321, C384–C394 (2021).

        70.Jugder, B. E., Kamareddine, L. & Watnick, P. I. Microbiota-derived acetate activates intestinal innate immunity via the Tip60 histone acetyltransferase complex. Immunity 54, 1683-1697.e3 (2021).

        71.Rohs, P. D. A. et al. Identification of Potential Regulatory Domains within the MreC and MreD Components of the Cell Elongation Machinery. Journal of Bacteriology 203, (2021).

        72.Sher, J. W., Lim, H. C. & Bernhardt, T. G. Polar growth in corynebacterium glutamicum has a flexible cell wall synthase requirement. mBio 12, (2021).

        73.Lonfat, N. et al. Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development (Cambridge) 148, (2021).

        74.Lin, T. et al. Pseudomonas aeruginosa–induced nociceptor activation increases susceptibility to infection. PLoS Pathogens 17, (2021).

        75.He, Y., Zhang, M., Song, J. & Warman, M. L. Cell depleted areas do not repopulate after diphtheria toxin-induced killing of mandibular cartilage chondrocytes. Osteoarthritis and Cartilage 29, 1474–1484 (2021).

        76.Agarwal, R. et al. Filamin C Cardiomyopathy Variants Cause Protein and Lysosome Accumulation. Circulation Research 129, 751–766 (2021).

        77.Wan, G. et al.  ZSP‐1 is a Z granule surface protein required for Z granule fluidity and germline immortality in Caenorhabditis elegans . The EMBO Journal 40, (2021).

        78.Yan, Y. et al. Interleukin-6 produced by enteric neurons regulates the number and phenotype of microbe-responsive regulatory T cells in the gut. Immunity 54, 499-513.e5 (2021).

        79.Voisin, T. et al. The CysLT2R receptor mediates leukotriene C4-driven acute and chronic itch. Proceedings of the National Academy of Sciences of the United States of America 118, (2021).

        80.Adeyemi, R. O. et al. The Protexin complex counters resection on stalled forks to promote homologous recombination and crosslink repair. Molecular Cell 81, 4440-4456.e7 (2021).

        81.Warr, A. R., Kuehl, C. J. & Waldor, M. K. Shiga toxin remodels the intestinal epithelial transcriptional response to Enterohemorrhagic Escherichia coli. PLoS Pathogens 17, (2021).

        82.Senft, R. A., Freret, M. E., Sturrock, N. & Dymecki, S. M. Neurochemically and hodologically distinct ascending VGLUT3 versus serotonin subsystems comprise the r2-pet1 median raphe. Journal of Neuroscience 41, 2581–2600 (2021).

        83.Mysore, V. et al. FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. Nature Communications 12, (2021).

        84.Roehle, K. et al. cIAP1/2 antagonism eliminates MHC class I–negative tumors through T cell–dependent reprogramming of mononuclear phagocytes. Science Translational Medicine 13, (2021).

        85.Clark, L. E. et al. VLDLR and ApoER2 are receptors for multiple alphaviruses. Nature 602, 475–480 (2022).***

        86.rk, D., You, W. & Cepko, C. L. Mouse Lines with Cre-Mediated Recombination in Retinal Amacrine Cells. eNeuro 9, (2022).

        87.Xu, J. et al. through the use of epitope tags recognized by nanobodies. Elife 11, (2022).

        88.Jouandin, P. et al. Lysosomal cystine mobilization shapes the response of TORC1 and tissue growth to fasting. Science 375, eabc4203 (2022).

        89.Pal, R. et al. First Clinical Results of Fluorescence Lifetime-enhanced Tumor Imaging Using Receptor-targeted Fluorescent Probes. Clin Cancer Res 28, 2373–2384 (2022).

        90.Xia, Y. et al. /AEP pathway shortens life span via selective GABAnergic neuronal degeneration by FOXO repression. Sci Adv 8, eabj8658 (2022).

        91.Mann, A. O. et al. T cells promote muscle regeneration in a microbiota-dependent manner. J Exp Med 219, (2022).

        92.Gao, Y. et al. The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination. Genes Dev 36, 634–646 (2022).

        93.Xu, J. et al. Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing. Proc Natl Acad Sci U S A 119, e2203179119 (2022).

        94.Reichart, D. et al. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 377, eabo1984 (2022).

        95.Ghosh, A. C. et al. Modeling exercise using optogenetically contractible Drosophila larvae. BMC Genomics 23, 623 (2022).

        96.Navarro, P. P. et al. Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli. Nat Microbiol 7, 1621–1634 (2022).***

        97.Jugder, B. E. et al. Vibrio cholerae high cell density quorum sensing activates the host intestinal innate immune response. Cell Rep 40, 111368 (2022).

        98.Kishi, J. Y. et al. Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. Nat Methods 19, 1393–1402 (2022).

        99.Goodwin, D. R. et al. Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics. bioRxiv 2022.07.31.502046 (2022) doi:10.1101/2022.07.31.502046.

        100.Aymonnier, K. et al. Inflammasome activation in neutrophils of patients with severe COVID-19. Blood Advances 6, 2001–2013 (2022).

        101.Dingus, J. G., Tang, J. C. Y., Amamoto, R., Wallick, G. K. & Cepko, C. L. A general approach for stabilizing nanobodies for intracellular expression. eLife 11, (2022).

        102.Aytürk, D. G., You, W. & Cepko, C. L. Mouse Lines with Cre-Mediated Recombination in Retinal Amacrine Cells. eNeuro 9, (2022).

        103.Xu, J. et al. Protein visualization and manipulation in Drosophila through the use of epitope tags recognized by nanobodies. eLife 11, (2022).

        104.Bosch, J. A. et al. Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila. eLife 11, (2022).

        105.Kim, A. R. et al. NanoTag Nanobody Tools for Drosophila In Vitro and In Vivo Studies. Current Protocols 2, (2022).

        106.McKitterick, A. C. & Bernhardt, T. G. Phage resistance profiling identifies new genes required for biogenesis and modification of the corynebacterial cell envelope. eLife 11, (2022).

        107.Flores-Kim, J., Dobihal, G. S., Bernhardt, T. G. & Rudner, D. Z. WhyD tailors surface polymers to prevent premature bacteriolysis and direct cell elongation in Streptococcus pneumoniae. eLife 11, (2022).

        108.West, E. R. et al. Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity. Cell Reports 38, (2022).

        109.Amamoto, R., Wallick, G. K. & Cepko, C. L. Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration. eLife 11, (2022).

        110.Dobihal, G. S., Flores-Kim, J., Roney, I. J., Wang, X. & Rudner, D. Z. The WalR-WalK Signaling Pathway Modulates the Activities of both CwlO and LytE through Control of the Peptidoglycan Deacetylase PdaC in Bacillus subtilis. Journal of Bacteriology 204, (2022).

        111.Tomizawa, R. R., Tabin, C. J. & Atsuta, Y. In ovo electroporation of chicken limb bud ectoderm: Electroporation to chick limb ectoderm. Developmental Dynamics 251, 1628–1638 (2022).

        112.Amon, J. D., Artzi, L. & Rudner, D. Z. Genetic Evidence for Signal Transduction within the Bacillus subtilis GerA Germinant Receptor. Journal of Bacteriology 204, (2022).

        113.Xia, Y. et al. Neuronal C/EBPβ/AEP pathway shortens life span via selective GABAnergic neuronal degeneration by FOXO repression. Science Advances 8, (2022).

        114.Brunet, Y. R., Habib, C., Brogan, A. P., Artzi, L. & Rudner, D. Z. Intrinsically disordered protein regions are required for cell wall homeostasis in Bacillus subtilis. Genes and Development 36, 970–984 (2022).

        115.Sassone-Corsi, M. et al. Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts. Proceedings of the National Academy of Sciences of the United States of America 119, (2022).

        116.Michelson, D. A., Hase, K., Kaisho, T., Benoist, C. & Mathis, D. Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells. Cell 185, 2542-2558.e18 (2022).

        117.Larson, R. C. et al. CAR T cell killing requires the IFNγR pathway in solid but not liquid tumours. Nature 604, 563–570 (2022).***

        118.Uchida, A. M. et al. Tissue eosinophils express the IL-33 receptor ST2 and type 2 cytokines in patients with eosinophilic esophagitis. Allergy: European Journal of Allergy and Clinical Immunology 77, 656–660 (2022).

        119.Baldominos, P. et al. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche. Cell 185, 1694-1708.e19 (2022).***

        120.Baldominos, P. et al. Protocol to isolate live single cells while retaining spatial information by combining cell photolabeling and FACS. STAR Protocols 3, (2022).***

        121.Michelson, D. A., Benoist, C. & Mathis, D. CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance. Proceedings of the National Academy of Sciences of the United States of America 119, (2022).

        122.Mann, A. O. et al. IL-17A–producing γδT cells promote muscle regeneration in a microbiota-dependent manner. Journal of Experimental Medicine 219, (2022).

        123.Yang, N. J. et al. Anthrax toxins regulate pain signaling and can deliver molecular cargoes into ANTXR2+ DRG sensory neurons. Nature Neuroscience 25, 168–179 (2022).

        124.Agarwal, R. et al. Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3, an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere. Circulation 146, 1674–1693 (2022).

        125.Yang, D. et al. Nociceptor neurons direct goblet cells via a CGRP-RAMP1 axis to drive mucus production and gut barrier protection. Cell 185, 4190-4205.e25 (2022).***

        126.Ewen-Campen, B. et al. split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80. Proc Natl Acad Sci U S A 120, e2304730120 (2023).

        127.Peters, C. W. et al. Rescue of hearing by adenine base editing in a humanized mouse model of Usher syndrome type 1F. Mol Ther 31, 2439–2453 (2023).

        128.Pal, R. et al. Fluorescence lifetime of injected indocyanine green as a universal marker of solid tumours in patients. Nat Biomed Eng 7, 1649–1666 (2023).

        129.He, L. & Perrimon, N. Synthetic Notch receptors and their applications to study cell-cell contacts in vivo. Developmental Cell 58, 171–173 (2023).

        130.David, L. et al. Piezo mechanosensory channels regulate centrosome integrity and mitotic entry. Proceedings of the National Academy of Sciences of the United States of America 120, (2023).

        131.Li, Y. et al. Gut AstA mediates sleep deprivation-induced energy wasting in Drosophila. Cell Discovery 9, (2023).

        132.Xu, C. et al. A phosphate-sensing organelle regulates phosphate and tissue homeostasis. Nature 617, 798–806 (2023).

        133.Roney, I. J. & Rudner, D. Z. Two broadly conserved families of polyprenyl-phosphate transporters. Nature 613, 729–734 (2023).

        134.Coleman-Gosser, N. et al. Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research. eLife 12, (2023).

        135.Xue, Y. et al. Chromophore supply modulates cone function and survival in retinitis pigmentosa mouse models. Proceedings of the National Academy of Sciences of the United States of America 120, (2023).

        136.Petsakou, A. et al. Cholinergic neurons trigger epithelial Ca2+ currents to heal the gut. Nature 623, 122–131 (2023).

        137.Gao, Y. et al. Bacterial spore germination receptors are nutrient-gated ion channels. Science 380, 387–391 (2023).

        138.Saavedra, P. et al. REPTOR and CREBRF encode key regulators of muscle energy metabolism. Nature Communications 14, (2023).

        139.Fivenson, E. M. et al. A role for the Gram-negative outer membrane in bacterial shape determination. Proceedings of the National Academy of Sciences of the United States of America 120, (2023).

        140.Roney, I. J. & Rudner, D. Z. The DedA superfamily member PetA is required for the transbilayer distribution of phosphatidylethanolamine in bacterial membranes. Proceedings of the National Academy of Sciences of the United States of America 120, (2023).

        141.Zirin, J. et al. Expanding the Drosophila toolkit for dual control of gene expression. bioRxiv : the preprint server for biology (2023) doi:10.1101/2023.08.15.553399.

        142.Cepeda Diaz, A. K., Rudlaff, R. M., Farringer, M. & Dvorin, J. D.  Essential function of alveolin Pf IMC1g in the Plasmodium falciparum asexual blood stage . mBio 14, (2023).

        143.Michelson, D. A., Zuo, C., Verzi, M., Benoist, C. & Mathis, D. Hnf4 activates mimetic-cell enhancers to recapitulate gut and liver development within the thymus. Journal of Experimental Medicine 220, (2023).

        144.Brandstadter, J. D. et al. A novel cryopreservation and biobanking strategy to study lymphoid tissue stromal cells in human disease. European Journal of Immunology 53, (2023).

        145.Neel, D. v. et al. Gasdermin-E mediates mitochondrial damage in axons and neurodegeneration. Neuron 111, 1222-1240.e9 (2023).

        146.Zarin, P. et al. Treg cells require Izumo1R to regulate γδT cell-driven inflammation in the skin. Proceedings of the National Academy of Sciences of the United States of America 120, (2023).

        147.Quiat, D. et al. Damaging variants in FOXI3 cause microtia and craniofacial microsomia. Genetics in medicine : official journal of the American College of Medical Genetics 25, 143–150 (2023).

        148.Hong, F. et al. Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels. Nature Methods (2023) doi:10.1038/S41592-023-02115-3.

        149.Meyer, K. et al. Impaired neural stress resistance and loss of REST in bipolar disorder. Molecular Psychiatry (2023) doi:10.1038/S41380-023-02313-7.

        150.Aron, L. et al. A neurodegeneration checkpoint mediated by REST protects against the onset of Alzheimer’s disease. Nature Communications 14, (2023).

        151.Avilés, E. C. et al. High temporal frequency light response in mouse retina is mediated by ON and OFF bipolar cells and requires FAT3 signaling. bioRxiv : the preprint server for biology (2023) doi:10.1101/2023.11.02.565326.

        152.Ivanchenko, M. v et al. PCDH15 Dual-AAV Gene Therapy for Deafness and Blindness in Usher Syndrome Type 1F. bioRxiv : the preprint server for biology (2023) doi:10.1101/2023.11.09.566447.

        153.Podestà, M. A. et al. Stepwise differentiation of follicular helper T cells reveals distinct developmental and functional states. Nature communications 14, (2023).

        154.Yang, P. et al. Structural basis for VLDLR recognition by eastern equine encephalitis virus. bioRxiv : the preprint server for biology (2023) doi:10.1101/2023.11.14.567065.

        155.Törk, L., Moffatt, C. B., Bernhardt, T. G., Garner, E. C. & Kahne, D. Single-molecule dynamics show a transient lipopolysaccharide transport bridge. Nature 623, 814–819 (2023).

        156.Shlosman, I. et al. Allosteric activation of cell wall synthesis during bacterial growth. Nature communications 14, 3439 (2023).

        157.Midonet, C. et al. MacP bypass variants of Streptococcus pneumoniae PBP2a suggest a conserved mechanism for the activation of bifunctional cell wall synthases. mBio 14, e0239023 (2023).

        158.Bartlett, T. M. et al. Identification of FacZ as a division site placement factor in Staphylococcus aureus. bioRxiv : the preprint server for biology (2023) doi:10.1101/2023.04.24.538170.

        159.Chung, H.-L. et al. Very-long-chain fatty acids induce glial-derived sphingosine-1-phosphate synthesis, secretion, and neuroinflammation. Cell metabolism 35, 855-874.e5 (2023).

        160.Nardone, C. et al. A central role for regulated protein stability in the control of TFE3 and MITF by nutrients. Molecular cell 83, 57-73.e9 (2023).

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        163.Schmied, C. et al. Community-developed checklists for publishing images and image analyses. Nature Methods (2023) doi:10.1038/s41592-023-01987-9.

        164.Senft, R. A. et al. A biologist’s guide to planning and performing quantitative bioimaging experiments. PLOS Biology 21, e3002167- (2023).

        165.Huang, Y. et al. EZH2 Cooperates with BRD4-NUT to Drive NUT Carcinoma Growth by Silencing Key Tumor Suppressor Genes. Cancer Research 83, 3956–3973 (2023).***

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        176.LaFleur, M. W. et al. X-CHIME enables combinatorial, inducible, lineage-specific and sequential knockout of genes in the immune system. Nature immunology 25, 178–188 (2024).


    Publications authored by MicRoN Staff (as microscopists) 

        1.Montero Llopis, P. et al. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nature Methods vol. 18 1463–1476 at https://doi.org/10.1038/s41592-021-01156-w (2021).

        2.Ryan, J. et al. MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. Nature Methods 18, 1414–1416 (2021).

        3.Rigano, A. et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nature Methods 18, 1489–1495 (2021).

        4.Montero Llopis, P., Stephansky, R. & Wang, X. High-Throughput Imaging of Bacillus subtilis. Methods in molecular biology (Clifton, N.J.) 2476, 277–292 (2022).

        5.Senft, R. A. et al. A biologist’s guide to planning and performing quantitative bioimaging experiments. PLOS Biology 21, e3002167- (2023).

        6.Schmied, C. et al. Community-developed checklists for publishing images and image analyses. Nature Methods (2023) doi:10.1038/s41592-023-01987-9.




  • Information for your grant or fellowship

    Grants and fellowships that require a description of the core and its services: Please use the information below.

    "MicRoN is a light microscopy core at Harvard Medical School, supporting more 150 groups in the Longwood Medical area. The core currently supports a wide range of disciplines, including bacterial cell biology, neurobiology, gene therapy development, limb regeneration, immune cell function, cancer immunotherapy, and the development of new tools and genetic models to investigate human disease, aging, and tissue architecture.

    MicRoN is equipped with state-of-the-art instrumentation to support most microscopy modalities and imaging needs:

    • Widefield (4x Nikon Ti or Ti2 inverted microscopes outfitted with a live cell imaging environmental enclosure)
    • TIRF: Nikon Ti with notorized TIRF arm and
    • Spinning disk: 2x Yokogawa CSU-1 scan units on a Nikon Ti or Ti2 inverted stand with a full incubator enclosure. One of the spinning disks is outfitted with a Digital Mirror Device (DMD), for optogenetics.
    • Single point scanning confocal and multiphoton: Zeiss LSM780, Zeiss LSM 980 + AiryScan2 (outfitted with live cell imaging enclosure), Olympus FV3000, Leica Stellaris 8 DIVE FALCON upright (confocal and multiphoton; outfitted with live cell imaging enclosure).
    • FLIM (Fluorescence Lifetime Imaging Microscopy; confocal or multiphoton mode): Leica Stellaris 8 DIVE FALCON upright (confocal and multiphoton)
    • Super-resolution: N-SIM-TIRF structure illumination (2D-, 3D-, TIRF-SIM; outfitted with live cell imaging enclosure) and LSM980 +Airyscan2 (confocal; described above).
    • Slide-scanner: 9-slide widefield (brightfield, color and fluorescence) Nikon Ti inverted microscope.
    • High-Content: InCell 6000 + robotic arm (coming soon).

    The instruments described above, support FRAP (LSM980), long term live cell imaging (in both widefield, confocal and multiphoton modes, all widefields, spinning disk confocals, Zeiss LSM980, Leica Stellaris 8 DIVE), multiplexing imaging (Leica Stellaris 8 DIVE and Zeiss LSM980), and imaging of optically cleared samples (with refractive index matching, dipping lenses; Leica Stellaris 8 DIVE confocal and multiphoton). 

    The core offers tailored one-on-one trainings and support for our trainees, including experimental design, image optimization and data analysis. The dedicated PhD-level core staff assists and collaborates with our trainees in the development or implementation of new technologies facilitating their adoption and in creating custom image acquisition and analysis pipelines to improve imaging workflows and outcome. Finally, the core is committed to helping trainees build quantitative microscopy skills that are critical for a career in life sciences, focusing on rigor and reproducibility"

    Letters of support and assistance with the new NIH policy in Data Management and Sharing: Please contact MicRoN Director Paula Montero Llopis paula_monterollopis@hms.harvard. edu


  • Webinars and Online Tutorials

  • Software

  • MicRoN Big Dipper Image Analysis Work Station

    The MicRoN core is pleased to offer our users image analysis capabilities on a workstation built to handle large datasets. Included in our software portfolio are standard programs such as FIJI, MATLAB, R, CellProfiler, Python, icy, etc. Additionally, we have a full license for arivis Vision4D, a powerful commercial analysis program capable of multi-dimensional data analysis, visualization, and animation with image sets in the terabyte file size.


    To familiarize users with Vision4D we offer a 2-hour tutorial for $50 that will cover the following topics:

    • Data import and image visualization/navigation
    • Finding and viewing image metadata
    • Stitching multi-xy datasets
    • 4D viewing and high-resolution image rendering/video animation
    • An overview of the analysis capabilities and building of a template analysis pipeline for your dataset


    As part of this 2-hour tutorial users must provide a data set to work with for building template analysis pipelines. The template pipeline is not a comprehensive solution for your analysis but should provide a sufficient starting workflow to build on for image analysis.


    MicRoN staff is available to help you troubleshoot your analysis workflow, but currently we do not have the capability to create custom analysis. The core has access to remote support for more in-depth help from the Vision4D software team.


    The workstation is equipped with the following specifications:

    • Intel Xeon Platinum 8260 CPU – 24 cores at 2.4GHz
    • 196GB RAM
    • NVIDIA GeForce GTX 2080 Ti Graphics Card
    • 2TB NVMe hard drive for use during analysis
    • 12TB HDD for short term data storage
    • 38” monitor for high-res visualization
    • 10Gbit ethernet connection for fast server connections*


    *The analysis workstation is not meant for long term storage of data. Please be sure you have a backup copy of your data stored somewhere else. MicRoN is not responsible for loss of data due to hard drive failure. The workstation is equipped with direct server connections, including OMERO, for easy transfer of data.


    We currently have remote access capabilities for the workstation across all software programs. If this is something you would like to use, please let us know so we can get you set up.

  • Nanocourse Lectures

  • Microscopy Information and Education

  • Fluorophores and Fluorescent Proteins

  • Protocols and Sample Preparation


  • Harvard Training Portal