Imaging- Bright field
daniel.dautan daniel, Per Svenningsson
Abstract
Protocol for imaging using Hamamatsu NanoZoomer slide scanner. Sections for analysis should be mounted on slides, stained for appropriate markers, and coverslipped. This protocol is using a Carl Zeiss LSM 880 confocal microcope.
Steps
Image slides at 40x magnification.
Extract individual sections using the NDP.view software (https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html).
Save images as tiff files.
Open images from same structures as one single stack using the merge function.
Using the crop, rotate, and move functions align all
images from the same stack as best as possible. Note: Using 2-3 specific
anatomy points to align the structures make the process easier.
Crop the entire stack at the same dimensions.
Save each image as a new tiff file (it is recommended
to save it in a new folder).
Open the imageJ macro provided on Zenodo: https://doi.org/10.5281/zenodo.10822458.
Note: A README is provided at the beginning of the macro in order to convert all images in a 0-255 bit image.
Save the images as a new tiff file (it is recommended to save it
in a new folder).
Open matlab and run for each structure the protocol provided on the Zenodo: https://doi.org/10.5281/zenodo.10822458.
Note: Follow the information provided on the code to align images.
