The Histology and Light Microscopy Core provides technical assistance, training, consultation, and assistance with all aspects of experimental design, sample preparation, image processing, and data analysis. The core is equipped with state-of-the-art technologies and expertise in histology, high-resolution histological imaging, confocal microscopy, light sheet microscopy, spinning disk microscopy, and optical projection tomography.

Our team strives to provide you with the knowledge and equipment you need to perform your experiment successfully.

For optimal results, reach out to our staff in the planning stages of your experiments.

Biology is a beautiful thing, and we want to work with you to make it that way!

Contact

Blaise Ndjamen, PhD
Core Director
Email

 

Services Provided

  • Tissue processing, embedding, and sectioning (paraffin or frozen)
  • Histology analysis (e.g. H&E immunohistochemistry, immunofluorescence, TUNEL, RNAscope, tissue clearing)
  • Advanced Microscopy: confocal, spinning disk, light sheet, super-resolution, whole-slide scanning, and widefield microscopy
  • Quantitative Data and Image Analysis (using Imaris, Volocity, ImageJ/FIJI, MATLAB)
  • Training, consulting, and collaborations

Core Members

Michael Fleming
Research Technologist I

Minia Ghilamichael
Research Technologist I

Blaise Ndjamen
Core Director

Fengrong Yan
Senior Research Technologist

Capabilities

 

Histology: Histology can be a complicated and confusing subject. All steps from tissue dissection and fixation through processing, sectioning, and staining are important to get right. When tissue is removed from the body, there is a rapid activation of proteolytic enzymes involved with tissue decomposition. In order to view tissues in a state that is as “life-like” as possible, the tissue must be processed immediately. In most circumstances, this is done through immediate fixation using paraformaldehyde or formalin

Microscopy: The Microscopy team provides training and support services for independent users, as well as more advanced microscopy imaging services, 3D deconvolution and rendering, image analysis, and quantitation. Our staff provides consultation and assistance with all aspects of experimental design, sample preparation, imaging, data processing and analysis.

 
 

Quantitative Data and Image Analysis (using Imaris, Volocity, ImageJ/FIJI, MATLAB)

Training, Consultation & Collaboration

 

Fees and Scheduling

For more information on our fees, or to obtain a lab service agreement, contact us.

Scheduling

The Histology and Light Microscopy Core recharges researchers at an hourly rate for training and support with microscopes and sample preparation. Consult with our staff before preparing samples to ensure your reagents match the available equipment.

You are required to complete an initial training session before using any equipment in the core.

If you are part of UC San Francisco:

If you are part of a nonprofit institution or a private company:

  • Contact the core at histology@gladstone.ucsf.edu
  • Complete the lab service agreement and email it to the core
  • Create an account on iLab
  • Request services on iLab

To start your session with an already existing reservation:

  • To access your existing reservation, visit the equipment kiosk. Use your iLab credentials to log in.
  • Once logged in, you will see a list of your pre-scheduled reservations under “My kiosk sessions.”
  • Once you find your session, click the green “start” button. You will see the details of your reservation as well as a timer.
  • You may log out while your session is in process. To log out, click the upper right-hand side menu and select Log out. On the log out screen, you will see your list of Active sessions.

To start your session as a walk-in:

  • Log in to the core kiosk using your iLab credentials.
  • Select the instrument you would like to use from the menu.
  • Once a calendar of availability appears, select “create session." Choose your desired duration, and click “create session” again.
  • A new window will appear with the details for that reservation. You may be required to enter in your payment information and the equipment use type.
  • Once you fill out all the required information, click the start button to begin your session. After you click start, you will see a timer in the upper right-hand corner.
  • To navigate back to your list of sessions, click in the drop-down menu where you see your name and select “my reservations.”
  • To log out, click the upper right-hand side menu and select “Log out.” You may log out while your session is in process. On the log out screen, you will see your list of active sessions.

To end your session:

  • Login to the core kiosk using your iLab credentials.
  • Find your current reservation in the list under “My kiosk sessions” and click the blue finish button.
  • Confirm your action and click “finish session.” Your time on the instrument has been logged.

Recent Publications

Microglial microRNAs mediate sex-specific responses to tau pathology. A. Hsu, Q. Duan, S. McMahon, Y. Huang, S. A. Wood, N. S. Gray, B. Wang, B. G. Bruneau and S. M. Haldar. (2020). Salt-inducible kinase 1 maintains HDAC7 stability to promote pathologic cardiac remodeling. J Clin Invest, doi:10.1172/JCI133753 • L. Kodama, E. Guzman, J. I. Etchegaray, Y. Li, F. A. Sayed, L. Zhou, Y. Zhou, L. Zhan, D. Le, J. C. Udeochu, C. D. Clelland, Z. Cheng, G. Yu, Q. Li, K. S. Kosik and L. Gan (2020). Nat Neurosci. 23(2), 167–171. doi:10.1038/s41593-019-0560-7

Tau Reduction Prevents Key Features of Autism in Mouse Models. C. Tai, C. W. Chang, G. Q. Yu, I. Lopez, X. Yu, X. Wang, W. Guo and L. Mucke (2020). Neuron. doi:10.1016/j.neuron.2020.01.038

Single-Cell Determination of Cardiac Microtissue Structure and Function Using Light Sheet Microscopy. D. Turaga, O. B. Matthys, T. A. Hookway, D. A. Joy, M. Calvert and T. C. McDevitt (2020). Tissue Eng Part C Methods. doi:10.1089/ten.TEC.2020.0020

Self-Organized Pluripotent Stem Cell Patterning by Automated Design. D. Briers, A.R.G. Libby, I. Haghighi, D.A. Joy, B.R. Conklin, C. Belta, T.C. McDevitt (2019). Cell. doi:10.2139/ssrn.3318933

A Mac2-positive progenitor-like microglial population survives independent of CSF1R signaling in adult mouse brain. L.Zhan, P.D. Sohn, Y. Zhou, Y. Li, L. Gan (2019). bioRxiv. doi:10.1101/722090.

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. N.R. Stone, C.A. Gifford, R. Thomas, K.J.B. Pratt, K. Samse-Knapp, T.M.A. Mohamed, E.M. Radzinsky, A. Schricker, L. Ye, P. Yu, J.G. van Bemmel, K.N. Ivey, K.S.Pollard, D. Srivastava (2019). Cell Stem Cell. 25(1), 87–102.e9

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects. T.Y. de Soysa, S.S. Ranade, S. Okawa, S. Ravichandran, Y. Huang, H.T. Salunga, A. Schricker, A. del Sol, C.A. Gifford, D. Srivastava (2019). Nature. 572, 120–124.

Premature MicroRNA-1 Expression Causes Hypoplasia of the Cardiac Ventricular Conduction System. E. Samal, M. Evangelista, G, Galang, D. Srivastava, Y. Zhao, V. Vedantham (2019). Frontiers in Physiology. doi: 10.3389/fphys.2019.00235

Gladstone-led Publications

Fibrinogen in neurological diseases: mechanisms, imaging and therapeutics. M. A. Petersen, J. K. Ryu and K. Akassoglou (2018). Nat Rev Neurosci. 19(5), 283–301. doi:10.1038/nrn.2018.13 

Microglial microRNAs mediate sex-specific responses to tau pathology. L. Kodama, E. Guzman, J. I. Etchegaray, Y. Li, F. A. Sayed, L. Zhou, Y. Zhou, L. Zhan, D. Le, J. C. Udeochu, C. D. Clelland, Z. Cheng, G. Yu, Q. Li, K. S. Kosik and L. Gan (2020). Nat Neurosci. 23(2), 167–171. doi:10.1038/s41593-019-0560-7

Do Microglial Sex Differences Contribute to Sex Differences in Neurodegenerative Diseases? L. Kodama and L. Gan (2019). Trends Mol Med. 25(9), 741–749. doi:10.1016/j.molmed.2019.05.001 

Differential effects of partial and complete loss of TREM2 on microglial injury response and tauopathy. F. A. Sayed, M. Telpoukhovskaia, L. Kodama, Y. Li, Y. Zhou, D. Le, A. Hauduc, C. Ludwig, F. Gao, C. Clelland, L. Zhan, Y. A. Cooper, D. Davalos, K. Akassoglou, G. Coppola and L. Gan (2018). Proc Natl Acad Sci U S A. 115(40), 10172–10177. doi:10.1073/pnas.1811411115 

Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. L. Zhan, G. Krabbe, F. Du, I. Jones, M. C. Reichert, M. Telpoukhovskaia, L. Kodama, C. Wang, S. H. Cho, F. Sayed, Y. Li, D. Le, Y. Zhou, Y. Shen, B. West and L. Gan (2019). PLoS Biol. 17(2), e3000134. doi:10.1371/journal.pbio.3000134

Direct Reprogramming of Human Fibroblasts toward a Cardiomyocyte-like State. J.D. Fu, N.R. Stone, L. Liu, C.I Spencer, L. Qian, Y. Hayashi, P. Delgado-Olguin, S. Ding, B.G. Bruneau, D. Srivastava (2013). Stem Cell Reports. 1, 235–247 

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. N. R. Stone, C. A. Gifford, R. Thomas, K. J. B. Pratt, K. Samse-Knapp, T. M. A. Mohamed, E. M. Radzinsky, A. Schricker, L. Ye, P. Yu, J. G. van Bemmel, K. N. Ivey, K. S. Pollard and D. Srivastava (2019). Cell Stem Cell. 25(1), 87–102 e109. doi:10.1016/j.stem.2019.06.012 

Chemical Enhancement of In Vitro and In Vivo Direct Cardiac Reprogramming. T. M. Mohamed, N. R. Stone, E. C. Berry, E. Radzinsky, Y. Huang, K. Pratt, Y. S. Ang, P. Yu, H. Wang, S. Tang, S. Magnitsky, S. Ding, K. N. Ivey and D. Srivastava (2017). Circulation. 135(10), 978–995. doi:10.1161/CIRCULATIONAHA.116.024692 

Fibrinogen induces neural stem cell differentiation into astrocytes in the subventricular zone via BMP signaling. L. Pous, S. S. Deshpande, S. Nath, S. Mezey, S. C. Malik, S. Schildge, C. Bohrer, K. Topp, D. Pfeifer, F. Fernandez-Klett, S. Doostkam, D. K. Galanakis, V. Taylor, K. Akassoglou and C. Schachtrup (2020). Nat Commun. 11(1), 630. doi:10.1038/s41467-020-14466-y 

Imaging the dynamic interactions between immune cells and the neurovascular interface in the spinal cord. N. Borjini, E. Paouri, R. Tognatta, K. Akassoglou and D. Davalos (2019). Exp Neurol. 322(113046). doi:10.1016/j.expneurol.2019.113046 

Chromatin and epigenetics in development: a Special Issue. B. G. Bruneau, H. Koseki, S. Strome and M. E. Torres-Padilla (2019). Development. 146(19), doi:10.1242/dev.185025

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. A. L. Lind, Y. Y. Y. Lai, Y. Mostovoy, A. K. Holloway, A. Iannucci, A. C. Y. Mak, M. Fondi, V. Orlandini, W. L. Eckalbar, M. Milan, M. Rovatsos, I. G. Kichigin, A. I. Makunin, M. Johnson Pokorna, M. Altmanova, V. A. Trifonov, E. Schijlen, L. Kratochvil, R. Fani, P. Velensky, I. Rehak, T. Patarnello, T. S. Jessop, J. W. Hicks, O. A. Ryder, J. R. Mendelson, 3rd, C. Ciofi, P. Y. Kwok, K. S. Pollard and B. G. Bruneau (2019). Nat Ecol Evol. 3(8), 1241–1252. doi:10.1038/s41559-019-0945-8

CTCF confers local nucleosome resiliency after DNA replication and during mitosis. N. Owens, T. Papadopoulou, N. Festuccia, A. Tachtsidi, I. Gonzalez, A. Dubois, S. Vandormael-Pournin, E. P. Nora, B. G. Bruneau, M. Cohen-Tannoudji and P. Navarro (2019). Elife. 8, doi:10.7554/eLife.47898

RNA Interactions Are Essential for CTCF-Mediated Genome Organization. R. Saldana-Meyer, J. Rodriguez-Hernaez, T. Escobar, M. Nishana, K. Jacome-Lopez, E. P. Nora, B. G. Bruneau, A. Tsirigos, M. Furlan-Magaril, J. Skok and D. Reinberg (2019). Mol Cell. 76(3), 412–422 e415. doi:10.1016/j.molcel.2019.08.015

A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. M. A. H. Samee, B. G. Bruneau and K. S. Pollard (2019). Cell Syst. 8(1), 27–42 e26. doi:10.1016/j.cels.2018.12.001

Fibrinogen Activates BMP Signaling in Oligodendrocyte Progenitor Cells and Inhibits Remyelination after Vascular Damage. M. A. Petersen, J. K. Ryu, K. J. Chang, A. Etxeberria, S. Bardehle, A. S. Mendiola, W. Kamau-Devers, S. P. J. Fancy, A. Thor, E. A. Bushong, B. Baeza-Raja, C. A. Syme, M. D. Wu, P. E. Rios Coronado, A. Meyer-Franke, S. Yahn, L. Pous, J. K. Lee, C. Schachtrup, H. Lassmann, E. J. Huang, M. H. Han, M. Absinta, D. S. Reich, M. H. Ellisman, D. H. Rowitch, J. R. Chan and K. Akassoglou (2017). Neuron. 96(5), 1003–1012 e1007. doi:10.1016/j.neuron.2017.10.008

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. X. Yuan, M. Song, P. Devine, B. G. Bruneau, I. C. Scott and M. D. Wilson (2018). Nat Commun. 9(1), 4977. doi:10.1038/s41467-018-07451-z

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. C. M. Anderson, J. Hu, R. Thomas, T. B. Gainous, B. Celona, T. Sinha, D. E. Dickel, A. B. Heidt, S. M. Xu, B. G. Bruneau, K. S. Pollard, L. A. Pennacchio and B. L. Blac. (2017). Development. 144(7), 1235–1241. doi:10.1242/dev.138487

An open-source control system for in vivo fluorescence measurements from deep-brain structures. S. F. Owen and A. C. Kreitzer (2019). J Neurosci Methods. 311(170–177). doi:10.1016/j.jneumeth.2018.10.022

Thermal constraints on in vivo optogenetic manipulations. S. F. Owen, M. H. Liu and A. C. Kreitzer (2019). Nat Neurosci. 22(7), 1061–1065. doi:10.1038/s41593-019-0422-3

Regulation of Tau Homeostasis and Toxicity by Acetylation. T. Tracy, K. C. Claiborn and L. Gan (2019). Adv Exp Med Biol. 1184(47-55). doi:10.1007/978-981-32-9358-8_4

An Alzheimer’s-disease-protective APOE mutation. K. A. Zalocusky, M. R. Nelson and Y. Huang. (2019). Nat Med, 25(11), 1648-1649. doi:10.1038/s41591-019-0634-9 23.

Editorial overview: Neurobiology of disease (2018). C. Bagni and A. C. Kreitzer (2018). Curr Opin Neurobiol. 48(iv-vi). doi:10.1016/j.conb.2018.01.005

Converging pathways in neurodegeneration, from genetics to mechanisms. L. Gan, M. R. Cookson, L. Petrucelli and A. R. La Spada (2018). Nat Neurosci. 21(10), 1300–1309. doi:10.1038/s41593-018-0237-7

A Subpopulation of Striatal Neurons Mediates Levodopa-Induced Dyskinesia. A. E. Girasole, M. Y. Lum, D. Nathaniel, C. J. Bair-Marshall, C. J. Guenthner, L. Luo, A. C. Kreitzer and A. B. Nelson (2018). Neuron. 97(4), 787–795 e786. doi:10.1016/j.neuron.2018.01.017

Motor thalamus supports striatum-driven reinforcement. Lalive AL, Lien AD, Roseberry TK, Donahue CH, Kreitzer AC. Elife. 2018;7:e34032. Published 2018 Oct 8. doi:10.7554/eLife.34032

Spatiotemporal distribution of fibrinogen in marmoset and human inflammatory demyelination. N. J. Lee, S. K. Ha, P. Sati, M. Absinta, N. J. Luciano, J. A. Lefeuvre, M. K. Schindler, E. C. Leibovitch, J. K. Ryu, M. A. Petersen, A. C. Silva, S. Jacobson, K. Akassoglou and D. S. Reich (2018). Brain. 141(6), 1637–1649. doi:10.1093/brain/awy082

Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors. K. B. Manheimer, N. Patel, F. Richter, J. Gorham, A. C. Tai, J. Homsy, M. T. Boskovski, M. Parfenov, E. Goldmuntz, W. K. Chung, M. Brueckner, M. Tristani-Firouzi, D. Srivastava, J. G. Seidman, C. E. Seidman, B. D. Gelb and A. J. Sharp (2018). Hum Mutat. 39(6), 870–881. doi:10.1002/humu.23419

Fast-Spiking Interneurons Supply Feedforward Control of Bursting, Calcium, and Plasticity for Efficient Learning. S. F. Owen, J. D. Berke and A. C. Kreitzer (2018). Cell. 172(4), 683–695 e615. doi:10.1016/j.cell.2018.01.005

Pericytes: The Brain's Very First Responders? V. A. Rafalski, M. Merlini and K. Akassoglou (2018). Neuron. 100(1), 11–13. doi:10.1016/j.neuron.2018.09.033

Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration. J. K. Ryu, V. A. Rafalski, A. Meyer-Franke, R. A. Adams, S. B. Poda, P. E. Rios Coronado, L. O. Pedersen, V. Menon, K. M. Baeten, S. L. Sikorski, C. Bedard, K. Hanspers, S. Bardehle, A. S. Mendiola, D. Davalos, M. R. Machado, J. P. Chan, I. Plastira, M. A. Petersen, S. J. Pfaff, K. K. Ang, K. K. Hallenbeck, C. Syme, H. Hakozaki, M. H. Ellisman, R. A. Swanson, S. S. Zamvil, M. R. Arkin, S. H. Zorn, A. R. Pico, L. Mucke, S. B. Freedman, J. B. Stavenhagen, R. B. Nelson and K. Akassoglou (2018). Nat Immunol. 19(11), 1212–1223. doi:10.1038/s41590-018-0232-x

Military-related risk factors for dementia. H. M. Snyder, R. O. Carare, S. T. DeKosky, M. J. de Leon, D. Dykxhoorn, L. Gan, R. Gardner, S. R. Hinds, 2nd, M. Jaffee, B. T. Lamb, S. Landau, G. Manley, A. McKee, D. Perl, J. A. Schneider, M. Weiner, C. Wellington, K. Yaffe, L. Bain, A. M. Pacifico and M. C. Carrillo (2018). Alzheimers Dement. 14(12), 1651–1662. doi:10.1016/j.jalz.2018.08.011

A Genetically Encoded Fluorescent Sensor Enables Rapid and Specific Detection of Dopamine in Flies, Fish, and Mice. F. Sun, J. Zeng, M. Jing, J. Zhou, J. Feng, S. F. Owen, Y. Luo, F. Li, H. Wang, T. Yamaguchi, Z. Yong, Y. Gao, W. Peng, L. Wang, S. Zhang, J. Du, D. Lin, M. Xu, A. C. Kreitzer, G. Cui and Y. Li (2018). Cell. 174(2), 481–496 e419. doi:10.1016/j.cell.2018.06.042

Tau-mediated synaptic and neuronal dysfunction in neurodegenerative disease. T. E. Tracy and L. Gan (2018). Curr Opin Neurobiol. 51(134–138). doi:10.1016/j.conb.2018.04.027

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. A. J. Willsey, M. T. Morris, S. Wang, H. R. Willsey, N. Sun, N. Teerikorpi, T. B. Baum, G. Cagney, K. J. Bender, T. A. Desai, D. Srivastava, G. W. Davis, J. Doudna, E. Chang, V. Sohal, D. H. Lowenstein, H. Li, D. Agard, M. J. Keiser, B. Shoichet, M. von Zastrow, L. Mucke, S. Finkbeiner, L. Gan, N. Sestan, M. E. Ward, R. Huttenhain, T. J. Nowakowski, H. J. Bellen, L. M. Frank, M. K. Khokha, R. P. Lifton, M. Kampmann, T. Ideker, M. W. State and N. J. Krogan (2018). Cell. 174(3), 505–520. doi:10.1016/j.cell.2018.06.016

Klotho controls the brain-immune system interface in the choroid plexus. L. Zhu, L. R. Stein, D. Kim, K. Ho, G. Q. Yu, L. Zhan, T. E. Larsson and L. Mucke (2018). Proc Natl Acad Sci U S A. 115(48), E11388-E11396. doi:10.1073/pnas.1808609115

In Vivo Imaging of CNS Injury and Disease. K. Akassoglou, M. Merlini, V. A. Rafalski, R. Real, L. Liang, Y. Jin, S. E. Dougherty, V. De Paola, D. J. Linden, T. Misgeld and B. Zheng (2017). J Neurosci. 37(45), 10808–10816. doi:10.1523/JNEUROSCI.1826-17.2017

Core-led Publications

Single-Cell Determination of Cardiac Microtissue Structure and Function Using Light Sheet Microscopy. D. Turaga, O. B. Matthys, T. A. Hookway, D. A. Joy, M. Calvert and T. C. McDevitt (2020). Tissue Eng Part C Methods. doi:10.1089/ten.TEC.2020.0020

Lightsheet fluorescence microscopy of branching human fetal kidney. D. Isaacson, J. Shen, D. McCreedy, M. Calvert, T. McDevitt, G. Cunha and L. Baskin (2018). Kidney Int. 93(2), 525. doi:10.1016/j.kint.2017.09.010

Single-Cell Determination of Cardiac Microtissue Structure and Function Using Light Sheet Microscopy. D. Turaga, O. B. Matthys, T. A. Hookway, D. A. Joy, M. Calvert and T. C. McDevitt (2020). Tissue Eng Part C Methods. doi:10.1089/ten.TEC.2020.0020

Imaging the developing human external and internal urogenital organs with light sheet fluorescence microscopy. D. Isaacson, D. McCreedy, M. Calvert, J. Shen, A. Sinclair, M. Cao, Y. Li, T. McDevitt, G. Cunha and L. Baskin (2020). Differentiation. 111(12–21). doi:10.1016/j.diff.2019.09.006

Three-dimensional imaging of the developing human fetal urogenital-genital tract: Indifferent stage to male and female differentiation. D. Isaacson, J. Shen, M. Overland, Y. Li, A. Sinclair, M. Cao, D. McCreedy, M. Calvert, T. McDevitt, G. R. Cunha and L. Baskin (2018). Differentiation. 103(14–23). doi:10.1016/j.diff.2018.09.003

More Publications

Equipment

Learn how our experts can support your research.

Lightsheet/Single Plane Illumination Microscopy

Zeiss Z1 Light Sheet Microscope (Fin Whale)

Zeiss Z1 Light Sheet Microscope

What

  • Light Sheet Fluorescence Microscope
  • For both aqueous and cleared samples
  • Dual cameras for 2-color simultaneous acquisition (405nm, 488nm, 561nm, 640nm lasers)

Why

Sample requirements:

  • Typically embedded in agarose; either aqueous or pre-cleared (Clarity, PACT, etc.)
  • Samples usually fluorescently labeled
  • Sample preparation can require extensive optimization

Suitable applications:

  • High-speed fixed or live-cell imaging (>100fps)
  • Imaging large, thick samples at high resolution with extremely low-bleach, low phototoxicity
  • Long-term live-cell imaging (>6 hours)
  • Isotropic resolution- best possible 3D reconstruction

Not good for:

  • High magnification (max = 40x)
  • Simple experiments- time, labor, and data intensive!

Manufacturer Site

Confocal Microscopy

Olympus Fluoview FV3000 Confocal Microscope (Snow Leopard)
Leica SP5 inverted confocal microscope (Eagle}
Zeiss Cell Observer Spinning Disk Confocal Microscope (Hare)
Zeiss LSM880 with Airyscan (Tarsier)

Olympus Fluoview FV3000 Confocal Microscope

What

  • Point-scanning confocal microscope
  • Both Galvo & Resonance scanning for high speed imaging
  • Multiple laser lines (405nm, 445nm, 488nm, 514nm, 594nm, 561nm, 638nm)
  • Definite focus with Z drift correction function
  • Inverted microscope with motorized (x,y,Z) stage
  • >Incubation chamber (CO2, Temperature & Humidity) for both short & long live cell/tissue imaging

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates
  • Combo 35mm & Chambered slide holder
  • Both live & fixed tissues/cells

Applications:

  • Scanning confocal imaging for live and fixed -cell, organoid and tissue imaging
  • Live-cell fluorescence dynamics (i.e. FRAP, FRET, GCaMP)
  • Imaging individual cells at high resolution, any magnification
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Very thick samples (>100µm)
  • Very high-speed imaging (>10fps)

Manufacturer Site

Leica SP5 Inverted Confocal Microscope

What

  • Point-scanning inverted confocal microscope system
  • Laser (458nm, 488nm, 514nm, 543nm, 633nm) and metal halide illumination
  • Motorized stage and incubation (temperature control only)

Why

Sample types:

  • Chamber slides, 35mm dishes, or optical-quality well plates

Applications:

  • Fixed and live-cell confocal imaging
  • Up to 3 channels simultaneous acquisition
  • AOBS tunable beam-splitter for great flexibility with fluorophore combinations
  • Live-cell dynamics (FRAP, FRET, GCaMP)
  • Multipositional acquisition and tiling multiple images for large sample areas
  • Imaging individual cells at high magnification (63x, 100x)

Not good for:

  • Imaging DAPI or other dyes requiring 405nm excitation
  • Live-cell imaging requiring CO2 control
  • Very thick samples (>100µm)
  • Low-light fluorescence imaging
  • High-speed fluorescence imaging

Manufacturer Site

Zeiss Spinning Disk Confocal Microscope

What

  • Spinning disk confocal and wide-field epifluorescence system for live cell imaging.
  • Laser (405nm, 488nm, 561nm, 640nm), metal halide and LED illumination
  • Definite focus
  • DirectFRAP

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates

Applications:

  • High speed, live-cell confocal imaging
  • Live-cell dynamics (FRAP, FRET, GCaMP, FURA), imaging
  • Imaging individual cells at high magnification (63x, 100x)

Not good for:

  • Thick samples (>50um)
  • Low magnification, large field-of-view imaging

Manufacturer Site

Zeiss LSM880 Super-Resolution Confocal Microscope

What

  • Point-scanning confocal microscope
  • Airyscan detector for increased resolution (>120nm lateral), sensitivity
  • Multiple laser lines (405nm, 445nm, 488nm, 514nm, 561nm, 638nm)
  • Definite focus
  • Objective inverter for using dipping lenses

Why

Sample types:

  • Chamber slides, 35mm dishes or optical-quality well plates

Applications:

  • Scanning confocal imaging for mid-speed (13 fps) live-cell imaging
  • Live-cell fluorescent dynamics (i.e. FRAP, FRET, GCaMP)
  • Imaging individual cells at high resolution, any magnification
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Very thick samples (>100µm)
  • Very high-speed imaging (>10fps)

Manufacturer Site

Widefield Microscopy

Leica Versa 200 Slide Scanner (Octopus)
Nikon Eclipse E600 Upright Microscope (Chameleon)
Keyence Automated Epifluorescence Microscope (Coyote 1)
Keyence Inverted Epifluorescence Microscope (Coyote 2 and 3)
Zeiss AxioObserver Z1 inverted epifluorescence microscope (Cuttlefish)
Zeiss live cell inverted epifluorescense microscope (Tortoise)

Leica Versa 200 Automated Slide Scanner

What

  • Automated slide scanner with wide-field fluorescence and brightfield imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • High sensitivity RGB and monochrome camera
  • 5x, 10x, 20x, 40x air objectives and 63x oil objective (with auto-oiler)

Why

Sample types:

  • Slides

Applications:

  • Automated whole slide imaging for up to 200 slides per run
  • Multipositional acquisition and tiling for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Manufacturer Site

Nikon Eclipse E600 Upright Microscope

What

  • Wide-field upright epifluorescence and full-color brightfield imaging system
  • Metal halide illumination; filters for DAPI, FITC, and Texas Red
  • RGB and monochrome Retiga camera with Qcapture acquisition software

Why

Sample types:

  • Slides

Applications:

  • Epifluorescence and brightfield imaging for fixed samples

Not good for:

  • Live-cell imaging
  • Tissue cultures plates and dishes
  • Time-lapse microscopy
  • Low-light fluorescence imaging

Manufacturer Site

Keyence Automated Epifluorescence Microscope

What

  • Automated inverted wide-field epifluorescence and brightfield imaging system
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • High sensitivity RGB and monochrome camera

Why

Sample types:

  • Slides or 35mm dishes
  • Tissue culture plates
  • Petri dishes

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Multipositional acquisition and tiling multiple images for large sample areas
  • Structured illumination for increased resolution (pseudo-confocal)
  • Phase contrast and oblique illumination for high contrast brightfield imaging

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Manufacturer Site

Keyence Inverted Epifluorescence Microscope

What

  • Automated wide-field epifluorescence system
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5

Why

Sample types:

  • Slides or 35mm dishes

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Tiling multiple images for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)
  • Plastic tissue culture plates

Zeiss AxioObserver Z1 Inverted Microscope

What

  • Wide-field epifluorescence system for fixed and live-cell imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • Definite focus, motorized stage, and stable incubation (temperature and CO2 control)
  • Polarizing filter for imaging birefringence

Why

Sample types:

  • Slides, 35mm dishes, or tissue culture well plates

Applications:

  • Long-term live-cell imaging experiments
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • High-speed live-cell imaging
  • Thick samples (>50um)

Manufacturer Site

Zeiss AxioObserver Z1 Inverted Microscope

What

  • Wide-field inverted epifluorescence system for fixed and live cell imaging
  • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • Motorized stage and full incubation (temperature and CO2 control)
  • Flash4.0 sCMOS camera for low-light and high-speed imaging

Why

Sample types:

  • Slides, 35mm dishes, or tissue culture well plates

Applications:

  • Epifluorescence imaging for fixed and live-cell samples
  • Short term time-lapse imaging
  • Multipositional acquisition and tiling multiple images for large sample areas

Not good for:

  • Long term live-cell imaging
  • Thick samples (>50um)

Manufacturer Site

Tissue Clearing

LifeCanvas Active Tissue Clearing System (Jellyfish)

LifeCanvas Active Tissue Clearing System

What

  • EasyGel - Tissue Gel Hybridization System
  • Integrated temperature control and vacuum
  • 8 samples at once
  • SmartClear II - Active Clearing System
  • Maximum preservation of fluorescent protein (FP) signals
  • Based on stochastic electrotransport technology developed at MIT (Kim et al., PNAS, 2015)

Why

Sample types:

  • Fixed tissues > 500um

Manufacturer Site

 

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FAQs

Can I Get a Quote for My Project?

We will provide a quote once a request has been entered and confirmed.

What Type of Tissue Can Be Submitted to the Core Lab for Processing?

We accept a large variety of tissue types including regular soft tissues as well as bones, cells, and organoids pre-embedded in histogel or in suspension. All tissues must be fixed prior to submission.

Should I Fix My Samples Prior to Submitting Them to the Core, and What Is the Best Way to Fix Them?

Yes, all tissue should be fixed prior to submission. Most tissues do well with fresh perfusion followed by 4% PFA fixation overnight in the fridge. Common exceptions are brain and bone samples, which require extended fixation. Email us for more information.

How Do I Submit My Samples?

Formalin-fixed samples must be fixed for paraffin embedding (FFPE), and samples should be fixed and stored in 70% ethanol. To prepare cryo-samples, fixed tissues are submitted in 30% sucrose. The sample container must be leak-proof, and labeled with the iLab request track numbers.

Cassettes should be hand labeled with #2 pencil or solvent-resistant markers (we use the KP Marker Plus, from Scutek laboratories).

Let us know if you want your container returned, otherwise it will be recycled. You can provide your own slide boxes or purchase them from the core.

Any antibodies you provide must also be labeled.

Contact the core for the 10x Genomics Visium sample preparation

Can Samples Be Sent by Mail?

All samples must be dropped off in person.

When Will My Project Be Done?

The turn-around time is typically 10-15 working days, depending upon the size of the order and how many requests we have in our queue.

How Do I Know When My Samples Are Ready?

You will be noticed by iLab mail. Pick up by the drop-off area, in room 367 at Gladstone Institutes. Remember to pick up your antibodies as well!

Does the Core Provide Pathology Assessment?

Our core does not provide pathology assessment.

How Do I Pay for Services?

When you create an iLab account, you will provide a valid PO. We do not accept credit cards or cash.

Can I Use the Core Equipment (Scopes, Cryostat, Microtome) Independently?

All users must be trained by staff prior to accessing and using any equipment in the core.

How Do I Request Training?

First, set up an iLab account. Once you’ve created your account, fill out the instrument training request.

Once you send the request, it typically takes 1-2 weeks to schedule a training session.

Our training protocol is a 2-step process: the 1st session is more general and covers care and handling of the microscope. The 2nd session is more project-specific. At the end of these two training sessions, we then evaluate the comfort level of the trainee with the microscope before granting them the "assisted/dependent” (conditional access) or unassisted/independent user status with full access to the calendar.

How Do I Access the Core?

The core is located in room 367 at Gladstone Institutes. Our hours are Monday—Friday, 8:30am—5:00pm,

Instructions

Before entering the building, you must read Gladstone's COVID-19 safety protocol and attest that you have no symptoms and will adhere to Gladstone's COVID-19 protocols. 

Sign into reception in the lobby and the receptionist will call the core. For speedier entry to the building, email the core prior to your arrival and we will plan to meet you in the lobby to escort you.

When Should I Cite a Core Facility in a Publication, Presentation, or Poster?

We ask that you be generous with your citations. If you have any questions, reach out to one of the core managers.

Examples of when you should cite a core could include acknowledgement of:

  • Space
  • Equipment
  • Purchased core reagents/media
  • Services
  • If a core staff member assists you in the design or execution of your experiments