A Transcriptome Atlas Database for Mouse Embryo
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Auto Microscopy

Slides generated by the in situ hybridization robot are coverslipped and photographed in a light microscope equipped with a motorized stage (Image 2) that moves the slide in front of the objective. The equipment used consists of a Leica DM-RXA2 microscope, a motorized Märzhäuser stage that accommodates up to eight slides, a Leica electronic focusing system, a Hitachi CCD camera and a PC based controller that drives stage and camera.

Brain sections are too large to be photographed as a whole. Therefore, the motorized stage moves the sections in a stepwise fashion in front of the objective and at each step an image is taken. Each image is stored as a bitmap file and individual images are assembled into a mosaic image (Image 1) that is cropped, properly oriented and saved as TIFF file.

Resolution of images:

Magnification of objective Numerical aperture Micrometers per pixel
5x 0.15 3.2
10x 0.4 1.6

Image 1

Image 2