The Histology and Light Microscopy Core provides technical assistance, training, consultation, and collaboration for all aspects of experimental design, sample preparation, image processing, and data analysis. Our 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.

We strive to provide you with the knowledge and equipment you need to successfully perform your experiment. Our core also offers self service access for trained users.

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

Contact

If you have additional questions, check out our FAQs page. If you can’t find the answer to your question, reach out to us at histology@gladstone.ucsf.edu

Core Members

Marcella Foti
Research Technologist II

Rose Guerrero
Research Technologist III

Blaise Ndjamen
Core Director

Fengrong Yan
Senior Research Technologist

 

Services Provided

In addition to technical assistance and consultation on our services, we also provide training so that you can utilize the equipment on your own time.

Histology

  • Tissue processing (paraffin/FFPE and frozen/cryo)
  • Tissue embedding
  • Tissue sectioning
  • Tissue staining and whole slide scanning
    • H&E
    • IHC, IFA
    • ISH, TUNEL
    • Special staining (PAS, ORO, Congo Red, Masson's Trichrome)
    • Spatial Biology: 10x Visium, RNAscope

Advanced Microscopy

On live and fixed samples

  • Confocal/super-resolution
  • Spinning disk
  • Light-sheet, tissue clearing, volumetric imaging
  • Automated whole slide scanning
  • Widefield microscopy

Computer-Based Data Analysis

  • Mammoth: Imaris Workstation (Room 327)
    • Imaris Software
    • Stitchy Software “Stitching Software”
    • Imagescope, ImageJ/FIJI, OlyVia…
  • Gladstone Institute of Cardiovascular Disease Workstation
  • Gladstone Institute of Neurological Disease Workstation
  • Stereology: StereoInvestor

Training, consulting, and collaborations

Self-services: Equipment Usage (after training)

If you have additional questions, check out our FAQs.

 

Fees and Scheduling

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:

Microscope Reservation

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.

For questions, visit our FAQ page.

 

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

Fin Whale (Zeiss Z1 Light Sheet Microscope)

Fin Whale (Zeiss Z1 Light Sheet Microscope)Zeiss Z1 Light Sheet Microscope

  • Light Sheet Fluorescence Microscope
    • For both aqueous and cleared samples
    • Dual cameras for 2-color simultaneous acquisition (405nm, 488nm, 561nm, 640nm lasers)
  • 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)
    • Imaging large, thick samples at high resolution with extremely low-bleach, low phototoxicity
  • Does the core provide training on this equipment? Yes

Manufacturer Site

Confocal Microscopy

Snow Leopard (Olympus Fluoview FV3000)
Tarsier (Zeiss LSM880 Super-Resolution Confocal Microscope)
Hare (Zeiss Spinning Disk Confocal Microscope)
Eagle: Leica SP5 inverted confocal microscope

Snow Leopard (Olympus Fluoview FV3000)

  • Specifications:
    • 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
  • 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

Tarsier (Zeiss LSM880 Super-Resolution Confocal Microscope)

  • Specifications:
    • 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
  • Sample types:
    • Chamber slides
    •  
    • 35mm dishes
    • 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

Hare (Zeiss Spinning Disk Confocal Microscope)

  • Specifications:
    • 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
  • Sample types:
    • Chamber slides
    • 35mm dishes
    • 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)
  • Applications:Not good for:
    • Thick samples (>50um)
    • Low magnification, large field-of-view imaging

Manufacturer Site

Eagle (Leica SP5 Inverted Confocal Microscope)

  • Specifications:
    • Point-scanning inverted confocal microscope system
    • Laser (458nm, 488nm, 514nm, 543nm, 633nm) and metal halide illumination
    • Motorized stage and incubation (temperature control only)
  • Sample types:
    • Chamber slides
    • 35mm dishes
    • 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)

Manufacturer Site

Widefield Microscopy

Octopus: Leica Versa 200 Automated Slide Scanner
Coyote 1 (Keyence Automated Epifluorescence Microscope)
Coyote 2 and 3 (Keyence Inverted Epifluorescence Microscope)
Cuttlefish (Zeiss AxioObserver Z1 Inverted Microscope)
Tortoise (Zeiss Live Cell Inverted Epifluorescence Microscope)
Cameleon (Nikon Eclipse E600 Upright Microscope)

Octopus: Leica Versa 200 Automated Slide Scanner

  • Specifications:
    • 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)
  • Sample types:
    • Slides / high throughput
  • 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)
  • Does the core provide training on this equipment? Yes

Manufacturer Site

Coyote 1 (Keyence Automated Epifluorescence Microscope)

  • Specifications:
    • 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
  • 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

Coyote 2 and 3 (Keyence Inverted Epifluorescence Microscope)

  • Specifications:
    • Automated wide-field epifluorescence system
    • Metal halide illumination; filters for DAPI, GFP, RFP, and Cy5
  • Sample types:
    • Slides
    • 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

Manufacturer Site

Cuttlefish (Zeiss AxioObserver Z1 Inverted Microscope)

  • Specifications:
    • 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
  • Sample types:
    • Slides
    • 35mm dishes
    • 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

Tortoise (Zeiss Live Cell Inverted Epifluorescence Microscope)

  • Specifications:
    • 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
  • Sample types:
    • Slides
    • 35mm dishes
    • 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

Cameleon (Nikon Eclipse E600 Upright Microscope)

  • Specifications:
    • 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
  • 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

Tissue Processor: AS

Shandon Histocentre Cold Station
A82300001A Excelsior AS Tissue Processor with Line Conditioner

Shandon Histocentre Cold Station

  • Specifications:
    • Smart histology embedding module
    • Paraffin machine
    • Paraffin Wax embedding station
  • Sample types:
    • All types of tissues including fatty tissues
  • Applications:
    • Alcohol quality measurement enables you to extend your reagent life and provides significant cost savings
    • Automatic reagent rotation further extends reagent life using a proven system
  • Does the core provide training on this equipment? No

A82300001A Excelsior AS Tissue Processor with Line Conditioner

  • Specifications:
    • Automatically prepare tissue samples for laboratory testing, by fixing, dehydrating, clearing, and infiltrating them with paraffin
    • Enhanced tissue quality
    • Preheating reagents up to 35°C, minimizing tissue shock and facilitating reagent penetration
  • Sample types:
    • All types of tissues including fatty tissues
  • Applications:
    • Alcohol quality measurement enables you to extend your reagent life and provides significant cost savings
    • Automatic reagent rotation further extends reagent life using a proven system
  • Does the core provide training on this equipment? No

Manufacturer Site

Cassette Printer

Tissue-Tek SmartWrite

Sakura Tissue-Tek SmartWrite Thermal Cassette Printer 9022 with AutoLoader 9023

  • Specifications:
    • Thermal transfer printing technology that is noise, fume and UV cure-free.
    • Print quality is crisp, permanent and resistant to histological chemicals.
    • The reliable robotic cassette feed enables cassette printing every 7.5 seconds.
  • Applications:
    • These cassette printers also enable 300 dpi high-resolution and high-content 1D and 2D barcodes, alphanumeric, graphic and logo printing.
    • These cassette printers also enable 300 dpi high-resolution and high-content 1D and 2D barcodes, alphanumeric, graphic and logo printing.
    • The Tissue-Tek® SmartWrite® Software and drivers provide a single SMART solution for template design, printer management and LIS integration.
  • Does the core provide training on this equipment?

Manufacturer Site

Microtomes

Leica RM2245 Automatic Microtome

Leica RM2245 Automatic Microtome

  • Specifications:
    • The RM2245 is a semi-motorized rotary microtome, designed for routine in histopathology
    • Manual sectioning is enhanced by a high-precision motorized specimen feed, which results in efficient operation with maximum section quality and reproducibility
  • Application:
    • Choose between conventional, full-hand-wheel rotation, manual sectioning or "rocking mode".
    • Motorized sectioning and meets the many requirements of modern laboratories
  • Does the core provide training on this equipment? Yes

Cryostats

CryoStar NX50 Cryostat Instrument (Epredia)
CryoStar NX70 Cryostat Instrument (Epredia)

CryoStar NX50 Cryostat Instrument (Epredia)

  • Does the core provide training on this equipment? Yes

CryoStar NX70 Cryostat Instrument (Epredia)

  • Specifications:
    • A form-fitting design, integrated height control, and motorized sectioning
    • Adjustable cutting speed from 0 mm/s to 256 mm/s
    • Section thickness from 0.5 µm to 500 µm
    • Vertical stroke length of 64 mm
    • 48 mm horizontal feed range
    • 20 µm specimen retraction on return stroke, with optical indication
  • Applications:
    • Mounting tissue to ready-to-cut with quick freeze and setup features
    • Section tissue samples more efficiently with improved stability and individually controlled temperature settings on both the object holder and blade carrier
  • Does the core provide training on this equipment? No

Manufacturer Site

Stainer

Leica CV5030 Cover Slipper

Leica CV5030 Cover Slipper

  • Specifications
    • Integration into staining/coverslipping workstations to form a fully automated
    • Coverslips at a rate of 300 slides per hour using standard microscope slides and glass coverslips of different sizes to increase productivity and efficiency in the lab.

Manufacturer Site

Tissue Clearing

Jellyfish (LifeCanvas Active Tissue Clearing System)

Jellyfish (LifeCanvas Active Tissue Clearing System)

  • Specifications:
    • 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).
  • Sample types:
    • Fixed tissues > 500um

Manufacturer Site

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FAQs

How Do I Create an iLab Account?

If you're a UC San Francisco user, learn how to create an account with iLab.

If you’re part of a nonprofit organization or a for-profit company, you’ll need to sign a legal service agreement (LSA). Once the LSA is signed by both organizations, you’ll receive instructions on how to set up an iLab account to request services. Contact the core to start the LSA process.

How Can I Get a Quote for My Project?

  1. Login into your iLab account
  2. Initiate a service request
  3. Use the temporary PO number 11111 to finalize and submit your service request
  4. Email the core after your service request is submitted with the temporary PO to receive a formal quote
  5. Use the quote to generate a formal PO by your lab or organization’s financial department
  6. Use the valid PO to update your iLab account profile and billing or financial information
  7. Email the core a PDF copy of your formal PO

If you need help generating or submitting your PO, reach out to your lab’s grant or financial manager.

How Do I Get a Consultation?

Contact the core to schedule a consultation

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.

Who Can Access the Core’s Services and Instruments?

The core’s services are available to both Gladstone and outside researchers.

Can I Use the Core Equipment Independently?

Users can use some of the core equipment once they are trained and granted access by the core’s staff. Only formally trained users are allowed to use our core’s equipment.

What If I Already Have Experience Using Microscopes and Other Instruments?

In order to independently use the core’s microscopes and instruments, you must schedule a training session during which core staff will evaluate your experience and determine whether a second session is needed before gaining full access to the core’s equipment.

How Do I Request Services or Training?

Visit iLab and fill out the instrument training request. After you send the request, it typically takes 1–2 weeks to schedule a training session.

Our training protocol is a 2-step process. The first session is more general and covers care and handling of the microscope. The second session is focused on your specific project needs. At the end of these two training sessions, the core will evaluate your comfort level with the microscope before granting “assisted/dependent” or “unassisted/independent” user status with full access to the calendar.

How Do I Schedule or Make an Equipment Reservation?

Visit iLab to schedule a reservation.

How Do I Drop-Off and Pick-Up My Samples?

Sample drop-off
To drop off your samples, stop by the core located in room 367 at Gladstone Institutes, between 10am–3pm.

  • FFPE samples: 
    • You should fix your samples (in 4 percent PFA or 10 percent formalin), rinse (3x) in 1x PBS, and store in 70 percent EtOH, before bringing to the core.
    • Gradually increase EtOH ethanol concentration: 25 percent, 50 percent, and finally 70 percent EtOH approach is preferable or recommended.
  • Frozen tissues: Samples can be brought to the core in one of the following conditions:
    • In 30% sucrose (transported on ice)
    • In OCT blocks or tissues slides (transported on dried ice)

Contact the core for the 10x Genomics Visium sample preparation

Sample pick-up
The core will let you know when your samples are ready. When they are ready for pick up, stop by room 367 at Gladstone Institutes, between 10am–3pm.

Can Samples Be Sent by Mail?

All samples must be dropped off in person. To drop off your samples, stop by the core located in room 367 at Gladstone Institutes, between 10am–3pm

How Do I Know When My Samples Are Ready?

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

How Long Will It Take for My Request to Be Completed?

Standard turn-around time is typically 10–20 business days from the date the samples are dropped off and received by the core (not the project submission date via iLab), depending on the size of the order and how many requests we have in our queue.

Rush orderr turn-around is 5–10 days

Note that these are estimates and turn-around times can be longer due to the complexity and size of the project and our current workload.

Does the Core Provide Pathology Assessment?

Our core does not provide pathology assessment.

What Type of Tissue Can Be Submitted to the Core 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 percent PFA or 10 percent formalin fixation overnight in the fridge. Common exceptions are brain and bone samples, which require extended fixation.

Will Paraffin Blocks Be Returned after Completing the Request?

Yes.

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
 

Contact

If you have additional questions, check out our FAQs page. If you can’t find the answer to your question, reach out to us at histology@gladstone.ucsf.edu