Jul 15, 2024
Imaging- Bright field
- daniel.dautan daniel1,2,
- Per Svenningsson1,2
- 1Department of Clinical Neuroscience, Karolinska Institutet, 171 76 Stockholm, Sweden;
- 2Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
Protocol Citation: daniel.dautan daniel, Per Svenningsson 2024. Imaging- Bright field. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzjj9rlx1/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 04, 2024
Last Modified: September 23, 2024
Protocol Integer ID: 101202
Keywords: ASAPCRN
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: 020608
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.
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).
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.