Imaging Core

The Aga Khan University (Pakistan) hosts an imaging suite equipped with advanced imaging technologies and software, including:

  • Virtual Microscope

  • Confocal Microscope

  • Fluorescence Activated Cell Sorter


Imaging Suite
BSL-2 Laboratory, First Floor
Juma Building
Aga Khan University, Stadium Road


The facilities are accessible to AKU and non-AKU users at competitive rates for research purposes only.

Publications Policy

For publications that include data generated using equipment and software at the Imaging Core, it is mandatory to share the mansuscript with the relevant teams to ensure accurate reporting and interpretation of data.

Virtual Microscope

The virtual microscope creates digital images from routine glass slides, which can be viewed on computer monitors in a manner that simulates real observation sans the microscope. These images can be used for teaching, research, and archival use by researchers, shared by groups, and can be incorporated into teleconferences and digital pathology.


  • Whole slide scanning at 2x 10x, 20x, 40x

  • Z compression at 2x 10x, 20x, 40x

  • Z-stack at 2x 10x, 20x, 40x

  • Tissue Micro-Array 2x 10x, 20x, 40x

For queries and appointments
Dr Azhar Hussain​, Director

Confocal Microscope

A1R plus is a high-end point scanning confocal microscope. The system features a "hybrid scanner," a glavano scanner for high resolution up to 16 MP and a resonant scanner for ultrahigh speed imaging at 420fps (512 x 32 pixels). Using standard detector up to 4-color high resolution imaging can be performed by four lasers. Flourophore with overlapped spectra can be imaged using spectral detector.


    Four color confocal microscopy
    Multipoint and live time-lapse imaging
    Spectral detection and unmixing 
    Transmitted light Differential Interference Contrast (DIC)
    Up to 6 dimensional Imaging on Live and Fixed cells
    Fluorescence recovery after photobleaching (FRAP)
    Fluorescence Resonance Energy Transfer (FRET)
    Calcium Imaging

Instrument Specifications

    Inverted Nikon Ti E microscope
    Objectives 10x, 20x 40x dry objectives. 60x & 100x oil immersion
    Four  lasers: L1 - a solid state 640nm, L2 - a solid state 405nm, L3 - an Argon gas laser with                                      ​​457nm, 477nm, 488nm & 514nm laser lines and L4 - a solid state 561nm
    Four PMT detectors
    32 channel spectral detector
    Perfect focus system (PFS) for time lapse imaging
    Tokai Hit incubator for time lapse imaging
    NIS Elements software (AVI movies for time lapse)

For queries and appointments

Fluorescence Activated Cell Sorter

Flowcytometry is the measurement of cell properties in a flowing medium. It  can be used by researchers to carry outimmunophenotyping and analyse cell cycle and cellular material such as DNA and chromosomes from a range of cell types.


Orientation of the facility is mandatory for all users. Users will be briefed on the general principles of the flowcytometry and the guidelines of setting up their experiments. These sessions will be conducted by dedicated staff and faculty. The purpose of this training is to provide knowledge to users that will help them in designing their experiment efficiently and to use the facility effectively.

For queries and appointments

Abdul Wahab Siddiqui, Research Associate​


​​You can learn more about these equipments

Useful spectrum viewers

E-Learning (flowcytometry, software, and hardware theory