The CoreMarketplace: UTSW - Whole Brain Microscopy Facility

UT Southwestern Medical Center

5323 Harry Hines Blvd.

Dallas, TX 75390-8813

United States of America

https://www.utsouthwestern.edu/education/medical-school/departments/neurology/research/microscopy-facility/

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https://coremarketplace.org/FacilityID975 https://coremarketplace.org/RRID:SCR_017949

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https://utsw.corefacilities.org/service_center/3547/?tab=about

Primary Contact:

Denise Ramirez

Last Updated: More than One Year ago

Facility RRID

RRID:SCR_017949

Facility Details

The Whole Brain Microscopy Facility (WBMF) in the UT Southwestern Department of Neurology was established in 2014 and is supported by the Texas Institute for Brain Injury and Repair (TIBIR). The facility is particularly well-suited to advance the study of traumatic brain injury as well as other neurological and psychiatric disorders by utilizing cutting-edge microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. These techniques enable the tracing of neuronal projections from injured sites to their long-range targets, allowing crucial and previously unfeasible studies into the altered connections established by neurons following brain injury.

We provide access to several high-throughput microscopes for UT Southwestern and external researchers. WBMF houses two TissueVision TissueCyte 1000 instruments for the purpose of generating high-resolution, 3D renderings of entire rodent brains as well as two slide scanning microscopes (Hamamatsu Nanozoomer and Zeiss Axioscan.Z1) for the purpose of creating digital images of whole slides. We have dedicated computational science staff to perform automated quantitative image analysis at the whole brain or whole slide level. We also offer cryosectioning, general histological staining such as H&E, cresyl violet, or Luxol Fast Blue, and immunostaining.

Facility Policies

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Facility Equipment

Leica CM1950 Cryostat

The Leica CM1950 is a highly adaptable cryostat platform that can be tailor-made for each laboratory. By starting with the standard instrument and choosing from a range of options, every laboratory can have a clinical cryostat for their individual needs. Innovation and human-oriented features provide a cryostat with a new level of performance. The CM1950 is a high-performance cryostat with an encapsulated microtome and separate specimen cooling. It features a UV disinfection system, an (optional) integrated extraction system for section waste and an (optional) motor for motorized sectioning. The cryostat is designed to produce frozen sections for biological, medical and industrial applications. The CM1950 is suitable for in-vitro diagnostic (IVD) applications. [Product Link]

RRID:SCR_018061

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Leica VT1200S vibrating microtome

Fully automated Leica VT1200 S vibrating blade microtome is designed to meet the highest sectioning demands for cutting fresh and fixed tissue in Neuroscience. To achieve sections of the highest quality that retain viable cells on the section surface, the vertical deflection of the blade can be measured by Leica's Vibrocheck measurement device and minimised with the blade holder. The instrument was designed in collaboration with Prof. Dr. Peter Jonas and his group at the Physiology Department, Freiburg Germany. [Product Link]

RRID:SCR_020243

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TissueVision TissueCyte 1000 Photon Imaging System

Whole organ serial two photon tomography imaging platform that allows imaging of whole fixed organs based on high speed two photon microscopy TPM and integrated tissue sectioning. [Product Link]

RRID:SCR_018639

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ZEISS Axio Scan.Z1 Slide Scanner

Digitize your specimens with the Axio Scan.Z1 slide scanner and create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go. [Product Link]

RRID:SCR_020927

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Zeiss Axioscan.Z1
Hamamatsu Nanozoomer
Leica fluorescence stereomicroscope
Leica sliding microtome
MBF Bioscience Neurolucida 360
MBF Bioscience StereoInvestigator
Olympus Phaseview Lightsheet microscope

Publications

Publications associated with this facility (Click To View):

1.) Yang K, Torres-Ramirez G, Dobbs N, Han J, Asahina M, Fujinawa R, Song K, Liu Y, Lin W, Oviedo A, Chen C, Zhu L, Mueller WF, Lee K, Suzuki T, Yan N (2025 Jul 11). The STING pathway drives noninflammatory neurodegeneration in NGLY1 deficiency The Journal of Experimental Medicine, 222(10), e20242296. . PMCID: 12249164.

2.) Galvan M, Fujitani M, Heaselgrave SR, Thomas S, Chen B, Lee JJ, Wyler SC, Elmquist JK, Fujikawa T (2025 Feb 25). Development and Characterization of a Sf-1-Flp Mouse Model bioRxiv, (), 2025.02.21.639566. . PMCID: 11888304.

3.) Wanniarachchi HI, Schuetze R, Deng Y, Hamal KB, Pavlich CI, Tankoano PE, Tamminga C, Hammers H, Kapur P, Bueno LM, Rayas R, Wang T, Liu L, Trawick ML, Pinney KG, Mason RP (2025 Feb 24). Evaluating Therapeutic Efficacy of the Vascular Disrupting Agent OXi8007 Against Kidney Cancer in Mice Cancers, 17(5), 771. . PMCID: 11898701.

4.) Garza IT, Eller MM, Holmes SK, Schackmuth MK, Bailey RM (2024 Nov 5). Expression and distribution of rAAV9 intrathecally administered in juvenile to adolescent mice Gene Therapy, 32(3), 189-196. . PMCID: 12050342.

5.) Rodarte KE, Heyman SN, Guo L, Flores L, Savage TK, Villarreal J, Deng S, Xu L, Shah RB, Oliver TG, Johnson JE (2024 Nov 4). Neuroendocrine Differentiation in Prostate Cancer Requires ASCL1 Cancer research, 84(21), 3522-3537. . PMCID: 11534540.

6.) Poinsatte K, Kenwood M, Betz D, Nawaby A, Ajay AD, Xu W, Plautz EJ, Kong X, Ramirez DM, Goldberg MP (2024 Oct 10). SpinalTRAQ: A novel volumetric cervical spinal cord atlas identifies the corticospinal tract synaptic projectome in healthy and post-stroke mice bioRxiv, (), 2024.08.23.609434. . PMCID: 11482800.

7.) Salameh F, Lazzarini A, Kenkel J, Akgul Y (2024 Sep 24). The Impact of the Number and Duration of Treatments With a 1064 nm Diode Laser on Adipocyte Apoptosis: Implications for Noninvasive Fat Reduction Strategies Aesthetic Surgery Journal. Open Forum, 6(), ojae082. . PMCID: 11541045.

8.) Phinney NZ, Huang X, Toombs JE, Brekken RA (2024 Aug 17). Development of betabodies: The next generation of phosphatidylserine targeting agents The Journal of Biological Chemistry, 300(9), 107681. . PMCID: 11416255.

9.) Zhu M, Wang Y, Lu T, Guo J, Li L, Hsieh MH, Gopal P, Han Y, Fujiwara N, Wallace DP, Yu ASL, Fang X, Ransom C, Verschleisser S, Hsiehchen D, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H (2024 Aug 6). PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer. Cell metabolism, 36(8), 1711-1725.e8. doi: 10.1016/j.cmet.2024.05.015. PMID: 38901424.

10.) Tran DH, Kim D, Kesavan R, Brown H, Dey T, Soflaee MH, Vu HS, Tasdogan A, Guo J, Bezwada D, Al Saad H, Cai F, Solmonson A, Rion H, Chabatya R, Merchant S, Manales NJ, Tcheuyap VT, Mulkey M, Mathews TP, Brugarolas J, Morrison SJ, Zhu H, DeBerardinis RJ, Hoxhaj G (2024 Jul 11). De novo and salvage purine synthesis pathways across tissues and tumors. Cell, 187(14), 3602-3618.e20. . PMID: 38823389.

11.) Bennett ZT, Huang G, Dellinger MT, Sumer BD, Gao J (2024 Jul 2). Stepwise Ultra-pH-Sensitive Micelles Overcome a pK(a) Barrier for Systemic Lymph Node Delivery. ACS nano, 18(26), 16632-16647. doi: 10.1021/acsnano.4c00876. PMID: 38900677.

12.) Tappy EE, Ramirez DMO, Carrick KS, Pruszynski JE, Corton MM (2024 Jul). Somatic and autonomic nerve density and distribution within the clitoris: an immunohistochemical study in adult female cadavers. International urogynecology journal, 35(7), 1447-1456. doi: 10.1007/s00192-024-05811-6. PMID: 38819688.

13.) Krishnan V, Wu J, Mazumder AG, Kamen JL, Schirmer C, Adhyapak N, Bass JS, Lee SC, Maheshwari A, Molinaro G, Gibson JR, Huber KM, Minassian BA (2024 Jul). Clinicopathologic Dissociation: Robust Lafora Body Accumulation in Malin KO Mice Without Observable Changes in Home-Cage Behavior. The Journal of comparative neurology, 532(7), e25660. . PMID: 39039998.

14.) Eller MM, Zuberi AR, Fu X, Burgess SC, Lutz CM, Bailey RM (2024 Jun 13). Valine and Inflammation Drive Epilepsy in a Mouse Model of ECHS1 Deficiency bioRxiv, (), 2024.06.13.598697. . PMCID: 11195255.

15.) Tran DH, Kim D, Kesavan R, Brown H, Dey T, Soflaee MH, Vu HS, Tasdogan A, Guo J, Bezwada D, Saad HA, Cai F, Solmonson A, Rion H, Chabatya R, Merchant S, Manales NJ, Tcheuyap VT, Mulkey M, Mathews TP, Brugarolas J, Morrison S, Zhu H, DeBerardinis RJ, Hoxhaj G (2024 May 31). De novo and Salvage Purine Synthesis Pathways Across Tissues and Tumors Cell, 187(14), 3602-3618.e20. . PMCID: 11246224.

16.) Pal Choudhuri S, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Kim YJ, Gilbreath C, Zhong J, Phat S, Myers DT, Christensen CL, Mazloom-Farsibaf H, Stanzione M, Wong KK, Hung YP, Farago AF, Meador CB, Dyson NJ, Lawrence MS, Wu S, Drapkin BJ (2024 May 1). Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs. Cancer discovery, 14(5), 804-827. . PMID: 38386926.

17.) Vishlaghi N, Guo L, Griswold-Wheeler D, Sun Y, Booker C, Crossley JL, Bancroft AC, Juan C, Korlakunta S, Ramesh S, Pagani CA, Xu L, James AW, Tower RJ, Dellinger M, Levi B (2024 Apr 23). Vegfc-expressing cells form heterotopic bone after musculoskeletal injury. Cell reports, 43(4), 114049. doi: 10.1016/j.celrep.2024.114049. PMID: 38573853.

18.) Lim YZ, Zhu M, Wang Y, Sharma T, Kelley S, Oertling E, Zhu H, Corbitt N (2024 Mar 8). Pkd1l1-deficiency drives biliary atresia through ciliary dysfunction in biliary epithelial cells. Journal of hepatology, (), . pii: S0168-8278(24)00151-X. doi: 10.1016/j.jhep.2024.02.031. PMID: 38460793.

19.) Wyler S, Surbhi, Cao N, Merchant W, Bookout A, Gautron L (2024 Jan 25). Gpr149 is involved in energy homeostasis in the male mouse PeerJ, 12(), e16739. . PMCID: 10822134.

20.) Eglenen-Polat B, Kowash RR, Huang HC, Siteni S, Zhu M, Chen K, Bender ME, Mender I, Stastny V, Drapkin BJ, Raj P, Minna JD, Xu L, Shay JW, Akbay EA (2024 Jan 22). A telomere-targeting drug depletes cancer initiating cells and promotes anti-tumor immunity in small cell lung cancer. Nature communications, 15(1), 672. . PMID: 38253555.

21.) Ren W, Deng Y, Ward JD, Vairin R, Bai R, Wanniarachchi HI, Hamal KB, Tankoano PE, Tamminga CS, Bueno LMA, Hamel E, Mason RP, Trawick ML, Pinney KG (2024 Jan 5). Synthesis and biological evaluation of structurally diverse 6-aryl-3-aroyl-indole analogues as inhibitors of tubulin polymerization. European journal of medicinal chemistry, 263(), 115794. . PMID: 37984295.

22.) LaCroix MS, Artikis E, Hitt BD, Beaver JD, Estill-Terpack SJ, Gleason K, Tamminga CA, Evers BM, White CL 3rd, Caughey B, Diamond MI (2024 Jan). Tau seeding without tauopathy. The Journal of biological chemistry, 300(1), 105545. . PMID: 38072056.

23.) Gibson JM, Vazquez AH, Yamashiro K, Jakkamsetti V, Ren C, Lei K, Dentel B, Pascual JM, Tsai PT (2023 Dec 3). Cerebellar contribution to autism-relevant behaviors in fragile X syndrome models Cell reports, 42(12), 113533. . PMCID: 10831814.

24.) Tappy EE, Ramirez DMO, Stork AM, Carrick KS, Hamner JJ, Pruszynski JE, Corton MM (2023 Dec). Somatic and autonomic nerve density of the urethra, periurethral tissue, and anterior vaginal wall: an immunohistochemical study in adult female cadavers. International urogynecology journal, 34(12), 3023-3032. doi: 10.1007/s00192-023-05645-8. PMID: 37796330.

25.) Stallings NR, O'Neal MA, Hu J, Shen ZJ, Malter JS (2023 Oct 17). Long-term normalization of calcineurin activity in model mice rescues Pin1 and attenuates Alzheimer's phenotypes without blocking peripheral T cell IL-2 response. Alzheimer's research & therapy, 15(1), 179. . PMID: 37849016.

26.) Krishnan V, Wu J, Mazumder AG, Kamen JL, Schirmer C, Adhyapak N, Bass JS, Lee SC, Maheshwari A, Molinaro G, Gibson JR, Huber KM, Minassian BA (2023 Sep 13). Clinicopathologic Dissociation: Robust Lafora Body Accumulation in Malin KO Mice Without Observable Changes in Home-cage Behavior. bioRxiv : the preprint server for biology, (), . . PMID: 37745312.

27.) Ren W, Deng Y, Ward JD, Vairin R, Bai R, Wanniarachchi HI, Hamal KB, Tankoano PE, Tamminga CS, Bueno LM, Hamel E, Mason RP, Trawick ML, Pinney KG (2023 Sep 6). Synthesis and Biological Evaluation of Structurally Diverse 6-Aryl-3-Aroyl-Indole Analogues as Inhibitors of Tubulin Polymerization European journal of medicinal chemistry, 263(), 115794. . PMCID: 11019941.

28.) Ramirez DM, Whitesell JD, Bhagwat N, Thomas TL, Ajay AD, Nawaby A, Delatour B, Bay S, LaFaye P, Knox JE, Harris JA, Meeks JP, Diamond MI (2023 May 24). Endogenous pathology in tauopathy mice progresses via brain networks bioRxiv, (), 2023.05.23.541792. . PMCID: 10245958.

29.) Wang Z, Zhu S, Jia Y, Wang Y, Kubota N, Fujiwara N, Gordillo R, Lewis C, Zhu M, Sharma T, Li L, Zeng Q, Lin YH, Hsieh MH, Gopal P, Wang T, Hoare M, Campbell P, Hoshida Y, Zhu H (2023 Apr 10). Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease Cell, 186(9), 1968-1984.e20. . PMCID: 10321862.

30.) Cooley A, Madhukaran S, Stroebele E, Colon Caraballo M, Wang L, Akgul Y, Hon GC, Mahendroo M (2023 Feb 17). Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption. iScience, 26(2), 105953. . PMID: 36718364.

31.) Malone MK, Ujas TA, Britsch DR, Cotter KM, Poinsatte K, Stowe AM (2022 Nov 29). The immunopathology of B lymphocytes during stroke-induced injury and repair Seminars in Immunopathology, (), 1-13. . PMCID: 9708141.

32.) Mirbaha H, Chen D, Mullapudi V, Terpack SJ, White CL III, Joachimiak LA, Diamond MI (2022 Jun 22). Seed-competent tau monomer initiates pathology in a tauopathy mouse model The Journal of Biological Chemistry, 298(8), 102163. . PMCID: 9307951.

33.) Soflaee MH, Kesavan R, Sahu U, Tasdogan A, Villa E, Djabari Z, Cai F, Tran DH, Vu HS, Ali ES, Rion H, O’Hara BP, Kelekar S, Hallett JH, Martin M, Mathews TP, Gao P, Asara JM, Manning BD, Ben-Sahra I, Hoxhaj G (2022 May 16). Purine nucleotide depletion prompts cell migration by stimulating the serine synthesis pathway Nature Communications, 13(), 2698. . PMCID: 9110385.

34.) Gumusgoz E, Kasiri S, Guisso DR, Wu J, Dear M, Verhalen B, Minassian BA (2022 Apr). AAV-Mediated Artificial miRNA Reduces Pathogenic Polyglucosan Bodies and Neuroinflammation in Adult Polyglucosan Body and Lafora Disease Mouse Models. Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics, 19(3), 982-993. doi: 10.1007/s13311-022-01218-7. PMID: 35347645.

35.) Gibson JM, Howland CP, Ren C, Howland C, Vernino A, Tsai PT (2022 Mar 30). A Critical Period for Development of Cerebellar-Mediated Autism-Relevant Social Behavior The Journal of Neuroscience, 42(13), 2804-2823. . PMCID: 8973277.

36.) Snyder B, Wu HK, Tillman B, Floyd TF (2022 Jan 26). Aged Mouse Hippocampus Exhibits Signs of Chronic Hypoxia and an Impaired HIF-Controlled Response to Acute Hypoxic Exposures. Cells, 11(3), . . PMID: 35159233.

37.) Joseph DB, Henry GH, Malewska A, Reese JC, Mauck RJ, Gahan JC, Hutchinson RC, Malladi VS, Roehrborn CG, Vezina CM, Strand DW (2021 Oct). Single-cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions. The Journal of pathology, 255(2), 141-154. doi: 10.1002/path.5751. PMID: 34173975.

38.) Chu TT, Tu X, Yang K, Wu J, Repa JJ, Yan N (2021 Aug). Tonic prime-boost of STING signalling mediates Niemann-Pick disease type C. Nature, 596(7873), 570-575. doi: 10.1038/s41586-021-03762-2. PMID: 34290407.

39.) Joseph DB, Henry GH, Malewska A, Reese JC, Mauck RJ, Gahan JC, Hutchinson RC, Malladi VS, Roehrborn CG, Vezina CM, Strand DW (2021 Jul 22). Single cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions The Journal of pathology, 255(2), 141-154. . PMCID: 8429220.

40.) Ortega SB, Torres VO, Latchney SE, Whoolery CW, Noorbhai IZ, Poinsatte K, Selvaraj UM, Benson MA, Meeuwissen AJM, Plautz EJ, Kong X, Ramirez DM, Ajay AD, Meeks JP, Goldberg MP, Monson NL, Eisch AJ, Stowe AM (2020 Mar 3). B cells migrate into remote brain areas and support neurogenesis and functional recovery after focal stroke in mice. ID: 32051245.

41.) Jackson LA, Hare AM, Carrick KS, Ramirez DMO, Hamner JJ, Corton MM (2019 Nov). Anatomy, histology, and nerve density of clitoris and associated structures: clinical applications to vulvar surgery. ID: 31254525.

42.) Jackson LA, Ramirez DMO, Carrick KS, Pedersen R, Spirtos A, Corton MM (2019 May). Gross and Histologic Anatomy of the Pelvic Ureter: Clinical Applications to Pelvic Surgery. ID: 30969205.

43.) Poinsatte K, Betz D, Torres VO, Ajay AD, Mirza S, Selvaraj UM, Plautz EJ, Kong X, Gokhale S, Meeks JP, Ramirez DMO, Goldberg MP, Stowe AM (2019). Visualization and Quantification of Post-stroke Neural Connectivity and Neuroinflammation Using Serial Two-Photon Tomography in the Whole Mouse Brain. ID: 31636534.

44.) Hamner JJ, Carrick KS, Ramirez DMO, Corton MM (2018 Dec). Gross and histologic relationships of the retropubic urethra to lateral pelvic sidewall and anterior vaginal wall in female cadavers: clinical applications to retropubic surgery. ID: 30278172.

45.) Filatenkov A, Richardson TE, Daoud E, Johnson-Welch SF, Ramirez DM, Torrealba J, Greenberg B, Monson NL, Rajaram V (2017 Sep 27). Persistence of parenchymal and perivascular T-cells in treatment-refractory anti-N-methyl-D-aspartate receptor encephalitis. ID: 28777260.

46.) Rivas JR, Ireland SJ, Chkheidze R, Rounds WH, Lim J, Johnson J, Ramirez DM, Ligocki AJ, Chen D, Guzman AA, Woodhall M, Wilson PC, Meffre E, White C 3rd, Greenberg BM, Waters P, Cowell LG, Stowe AM, Monson NL (2017 Jan). Peripheral VH4+ plasmablasts demonstrate autoreactive B cell expansion toward brain antigens in early multiple sclerosis patients. ID: 27730299.

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ABRF

Association of Biomolecular Resource Facilities

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https://coremarketplace.org/?FacilityID=975
https://coremarketplace.org/RRID:SCR_017949

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Keywords:

Traumatic, brain, injury, neurological, psychiatric, disorder, microscopy, evaluate, neuropathy, stereological, analysis, neuron, tracing, 3D, rendering, dataset, service, core, ABRF

Resource Type:

access service resource, service resource, core facility

Citation:

Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility (RRID:SCR_017949)

UTSW - Whole Brain Microscopy Facility (Microscopy (Electron, Fluorescence, Optical))

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Associations

ABRF

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Metadata

SciCrunch Data Imports (data maintained by https://scicrunch.org)

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Contact Denise Ramirez

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UTSW - Whole Brain Microscopy Facility

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