Zeiss Stereology and Neurite Tracing

Zeiss Stereology Platform

New in 2022, the CMN Core Stereology and Neurite Tracing system is based on a Zeiss AxioImager M2 upright microscope equipped with a 5.3 MP sCMOS monochrome camera (for epifluorescence imaging) and a CMOS camera for brightfield image collection. The fully motorized microscope has a high precision motorized stage and optics that are optimized for epifluorescence and brightfield microscopy (no DIC).  Precise optical sectioning is achievable using the Apotome 3 structured illumination module.

Stereology is a method that allows the unbiased sampling of tissues for accurate counts or measurements of structures within tissue sections or flat samples (cover slips). Common examples of stereology include performing cell counts, measuring the lengths of blood vessels, axons or other linear structures within tissues, and estimating volumes of cells, lesions, infarcts or other structures. The CMN Core uses  MBF Biosciences StereoInvestigator software for Stereology and Neurolucida for Neurite tracing. The Core system can be used to perform live stereology or neurite tracing or it can be used to capture stereological data sets for evaluation on an analysis computer.

Available Magnifications (high NA Objectives):

Magnification Type Immersion NA Working Distance (mm)* Depth of Field (um), 488 nm
 2.5x EC Plan NeoFluar  AIR  0.085  8.8  98
 10X EC Plan NeoFluar  AIR  0.3  7.6  7.6
 20x EC Plan NeuoFluar  AIR  0.5  2.6  2.6
 40x Plan Apo  AIR  0.95  0.25**  1.84
 63x Plan Apo  OIL  1.4  0.14  0.68
 100x Plan Apo DIC  OIL  1.4  0.17  0.58

Fluorescence Filter Sets:

Fluorescence microscopy involves the excitation of fluorophores at a specific wavelength and the measurement of emitted light at another wavelength. The Zeiss Stereology system has the following fluorescent filters.

Channel Recommended Fluorophores  Excitation, nm
Dichroic, nm
Emission, nm
“Blue”  Dapi/Hoechst/AF405  390/40 (Violet)   FT 420  BP 450/40
“Green”  GFP/FITC/AF488  470/40 (Blue)  FT 495  BP: 525/50
“Red”  TRITC/RFP/DsRed/TdTomato/PI/Rhodamine/Cy3/AF546/AF555   550/25 (Green)  FT 570   605/70 (Red)
“Far Red”  Cy5/AF633/AF647/TO_PRO-3   640/30 (Red)  FT 660  690/50(Far Red)

Brightfield Microscopy

Brightfield microscopy is used to examine cells and tissues that can be visualized without fluorescence, e.g H&E, cresyl violet, DAB.

Example of H&E Stain
Example of H&E Stain
 Example of Cresyl Violet Stain
Example of Cresyl Violet Stain