Rat Spinal Cord

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Project Description

Our collaborators newly established an way of staining the activity in the endogenous opioid system in the rat spinal cord, and the aim of the project is to quantify the amount and localization of mRNA staining. We have developed image analysis approaches for quantifying the amount of cells with positive signals and associate those to manually outlined regions of interest within the spinal cord of rats. We have applied our new method for local adaptive thresholding based on ellipse fit to segment nuclei, and use ilastik to classify positive/negative cells.

Tags: Microscopy, model organisms and tissues