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Software
To stitch images with Fiji, use Plugins -> Stitching -> Grid/Collection Stitching
To align images with Fiji, import images one-by-one (in the correct order). Then click Image -> Stack -> Images to Stack. Then click Plugins -> Registration -> Linear Stack Alignment with SIFT. For best results, increase maximum image size to 2048px. The expected transformation is Rigid (i.e. translation and rotation).
Typically, an FFT method is used, decreasing window size from 1024x1024 to the window size of interest. The error in Exx will increase as the window size is decresed, so an error analysis should be carried out to determine the optimal sub-window size.
Our in-house data analysis package - https://github.com/MechMicroMan/DataAnalysisUtilities
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Download the package from the link above, and place in a directory
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Install Anaconda from here - https://www.anaconda.com/download/
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Put this file (https://www.dropbox.com/s/zntvsnfbrbm12k2/10-addToPath.py?dl=0) in the ~/.ipython/profile_default/startup/ directory, changing the path in the file to the location in which you placed DataAnalysisUtilities in Step 1
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Run the following commands in Terminal to install packages required by DataAnalysisUtilites
pip install peakutils
- To run the tool, use the command:
jupyter notebook
then browse to the DataAnalysisUtilities directory and select the notebook (.ipynb file)
Git is version control software to track changes to files/code. The university runs a course on the basics and notes from the course are available here: http://gcapes.github.io/git-course/.