Toolkit for 3D image processing and analysis.
Implemented to work on single-channel 3D tiffs (x,y,z). Each folder contains minimum example data to test implementation before running it on other data.
Codes to test the impact of different image preprocessing (e.g. filtering), segmentation (e.g. Otsu thresholds), and processing (e.g. edge detection) steps. These tests enable an overview about which steps could potentially work well with the examined data. For instance, would background removal would be appropriate for the data under examination?
For measurement of similarity between images (e.g. before and after image registration). Measurements: Sum of Squared Differences (SSD), Sum of Absolute Differences (SAD), Maximum of Absolute Differences (MAD), Mean Square Error (MSE), Structual Similarity Information (SSI), and Mutual Information (MI).