Reconstruction Data Files

Image, 512x512 image, montage of cerebellar cortex triple labeled for Hoescht stain (blue);neurofilament (green) and GFAP (red)
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Reconstruction Data Files, mosaic reconstructed with 10% overlap; image normalization performed using ImageJ
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High resolution montage of a sagittal section through the cerebellar cortex of an adult male rat (80g), triple-labeled to reveal nuclei (Hoescht stain, blue), neurofilaments (particularly concentrated in axons, green) and astroglia (glial fibrillary acidic protein, GFAP, red). This image is a maximum projection of the Z-stack through the tissue, and has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.

Technical Details

80µm thick sections were mounted in gelvitol using coverslips with a 1.0 µm thickness. Images were acquired with a BioRad RTS 2000MP Multiphoton microscope using a 40X 1.3NA oil immersion objective. This mosaic image was reconstructed with 10% overlap of individual images; image normalization was performed using ImageJ.

Biological Sources

NCBI Organism Classification
Rattus norvegicus
(Brown Rat)
Cell Type
Purkinje cell
cerebellar granule cell
Cellular Component
cell projection cytoplasm
cell body
neuronal cell body
neurofilament cytoskeleton

Biological Context

Biological Process
cerebellum structural organization


Tom Deerinck
Data Qualifiers
processed data
suitable for spatial measurements

Sample Preparation

formaldehyde fixed tissue
Relation To Intact Cell
vibratome-sectioned tissue


Spatial Axis Image Size Pixel Size
X 512px ——
Y 356px ——

Detailed Project Information                           hide

Project ID: P1188
Leader: Tom Deerinck
Collaborators: James Bouwer and Mark Ellisman and Maryann Martone
Description: Creation of high resolution large scale brain maps of protein expression
Experimental purpose: high resolution protein labeling map of selected brain regions
Species: rat
System: central nervous system
Organ: brain
Region: cerebellum
Product type: confocal
Instrument: Biorad Radiance 2000 Confocal
Start/End Dates: 7/4/2002 - unknown

Specimen Preparation                                     hide

Microscopy Product ID: 25
Image Basename: T071502
Protocol Description: triple labeling for neurofilament protein, GFAP and nuclei

Detailed Imaging Parameters                          hide

Light microscopy product
Coverslip thickness: 1.0 um
Lens magnification: 40.0 X
Numerical aperture: 1.3
Immersion medium: oil
Mounting medium: gelvatol

Imaging Product Types                                    hide

Optical Section
Optical Z resolution: 1.5 um
Cutting plane: transverse

*CIL – Cell Image Library accession number. Please use this to reference an image.