Histology and Imaging Services - Miami Project to Cure Paralysis

Overview of Services

The Miami Project has a microscopy and image analysis workspace on the 4th floor of the LPLC, designed to function as a core facility. There are three stereology workstations running Stereoinvestigator and Neurolucida software (MBF Bioscience) which provide unbiased stereological analysis of cell number, fiber and vessel length, neuron tracing, 3D brain mapping and imaging capabilities. Each stereology workstation is equipped with a CCD camera, LUDL motorized stage, mercury burner, DAPI, 488, 594 single and triple filters, 5X, 10X, 20X, 40X, 63X and 100X objectives based on either an Olympus BX51, Zeiss Axiovert 200M or Zeiss Axiophot 2 microscope. A Zeiss Axioplan 2 microscope equipped with XCite 120 light source, CCD camera and SPOT Basic imaging software is available for fluorescent viewing and image capture. A multi-head brightfield Olympus BX50 microscope is available and equipped with Olympus SC30 digital color camera and Olympus analysis getIT software for image capturing. An Olympus FV1000 confocal microscope with 5 channel detection and spectral unmixing modes is available and equipped with 458,488,514,543,635 nm laser lines. The LaVision Bio Tec Ultramicroscope, a light sheet microscope, is equipped with an sCMOS camera and variable magnification from .63X to 6.3X
The Image Analysis Facility provides one computer workstation equipped with a PathScan Enabler slide scanner and loaded with Neurolucida, ImageJ/Fiji, Adobe Photoshop CS6 and Microsoft Office. A second workstation used exclusively for ultramicroscope acquisitions is loaded with Imaris 8.0.2(Bitplane) software with Measurement Pro, Filament Tracer and ImarisVantage modules and Adobe Photoshop CS6 extended.


Rules & Regulations 2017


Contact M.S. Yan Shi with any questions


(305)243-8042  (786)223-7618


In order to ensure the best and long-lasting usage of shared equipment all Facility users should respect the following guidelines:


  • All staff, postdocs, grad students and undergrads who intend to use the Microscopy and Imaging Facility have to be introduced to M.S. Yan Shi by their supervisor.


  • Basic training in operating each microscope and software is mandatory and provided by M.S. Yan. All new users must prove knowledge of the facility rules and proficiency in using a microscope and software before being given approval for unsupervised use.


  • Training sessions must be scheduled a minimum of 48hrs in advance.


  • Each microscope workstation requires a training session. Do not attempt to use a workstation you were not trained on.


  • Access to summer students and undergraduate volunteers is limited to those with standing protocols and prepared slides. Summer students and undergrad volunteers are required to submit a short study description which outlines sample type, quantification method and expected completion date.


  • Use of the confocal and ultramicroscope is off-limits to undergrads and summer students.


  • We appreciate your use of our facility and ask that you please acknowledge the Microscopy and Imaging Facility of the Miami Project to Cure Paralysis at The University Of Miami Miller School of Medicine in all publications derived through the use of the facility or collaborations with the facility’s staff.


Imaging Core Hours of Operation


Normal hours




Undergrads + volunteers



  • Requests for extended late-night and weekend use of facilities must be approved by M.S. Shi. 24/7 badge access to the main core and Confocal is restricted and will be granted on a case by case basis as determined by M.S. Shi.







Equipment schedules for microscope workstations are available 72hrs in advance. Weekend schedules and late-night reservations require approval by Yan.  

  • Users can claim only ONE open time slot per day on the schedule in advance.
  • There are time limits on equipment reservations. Each lab can sign up only once per station/day in advance.
  • During heavy demand, the Core reserves the right to set a maximum number of daily/weekly hours of individual use.
  • Any time slot not reserved in advance becomes available daily at 9:00am on a first come first served basis.
  • Cancellations must be made with 24hr advance notice. Any cancellation after that time will incur the standard usage fee.
  • We understand that sometimes experiments don't work or emergencies arise, but we do ask that you notify M.S. Shi of any cancellations.
  • Excessive no-shows will result in restricted access. 
  • Workstation reservations are held for 15min before being open to other users. If you will be late, please notify M.S. Shi so that you do not lose your time slot.
  • The last person on the schedule is responsible for turning the system off. If the system is left on overnight the last person on that days schedule will be held responsible.  If you are the last person scheduled you are responsible for notifying Yan if you cancel to insure that the equipment is not left on overnight.  
  • Users may book within designated time slots:


Slot 1

Slot 2

Slot 3

Slot 4

Slot 5

WA, WC, WD, Pathscan













 Note: The ultramicroscope and Imaris workstation do not have designated time slots. Users can book up to 3 hrs on the ultramic and 2 hrs on Imaris.



  • It is mandatory for every user to fill out the log sheet before starting work and after work is completed for the day.
  • All collected images or data have to be removed from the computer hard drive “C “or “D” the same day. Files left on the hard drive may be deleted without warning!
  • Microscope rooms should not be crowded.
  • Internet use on workstation computers is NOT allowed 
  • No food or drink.
  • Workstations must remain clean and orderly.
  • Immersion oil must be cleaned off all objectives at the beginning and end of each session.
  • Ultramicroscope equipment must be properly cleaned. All spills must be reported.
  • Users are responsible for shutting down the equipment in the proper order.
  • Excessive violations will result in restricted access and use.




Users are required to confirm their charge accounts on iLab. 

Invoices and  submitted IDR’s are available in the Image Analysis Facility.



Group A


Confocal microscope FV1000


StereoInvestigator/Neurolucida/Zeiss 4Ch


Pathscan workstation


Group B




Imaris workstation


Additional equipment


Multi-head w/ camera

No charge

Zeiss- fluorescent viewing

No charge




Name Role Phone Email Location
Yan Shi
LPLC 4-08