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🧪 Reproducing the concept of Confocal Laser Scanning Microscope. Using Arduino and easily found materials. Generating images in Grayscale just for fun.
Imaging experiments in Biology often involve the acquisition of confocal z-stack images to quantify fluorescent signal in a biological sample. These z-stacks are usually analyzed using open-source programs such as FIJI, which are notoriously frustrating to work with, and do not facility intuitive high-throughput analysis of many images at once. Manual image analysis is labor-intensive, time-consuming, and prone to human error. I compiled two notebooks to streamline two of the most commonly performed tasks in the analysis of confocal z-stack images: the generation of "pretty" maximum projections, and the analysis of pixel values/ fluorescence from sum projections.
Semi-automated script for detection and quantification of c-Fos cells in IHC stained confocal stack images
[Pillow] Denoising Images retrieved from Confocal Calcium Imaging.
Python project using Pyimagej to filter images, quantify and analyse particles in mouse brain slices.