Microscopy tools

Image registration and stitching with SIFT

2D-SIFT-in-3D-Space is a ImageJ/Fiji plugin and is available on GitHub. It has been designed for the registration and the stitching of two tilted half image stacks from the same sample. For more informations on its parameterization, please see the user manual. Please read carefully our article in Computers in Biology and Medicine to understand how work the parameters.

For dummies, you can download the jar and add it to your "plugins" directory in ImageJ or Fiji. Then the plugin will appear as "2D_SIFT_in_3D_Space" in the Plugins menu.

Simulator of confocal laser scanning microscope images

This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion. Here is a data sample to test it.

Progressive intensity and gamma correction

Progressive_Intensity_and_Gamma_Correction is a ImageJ/Fiji plugin. It increases or decreases the intensity and/or gamma contrast of each section progressively depending on the depth in the 3D volume stack. It is available here.

Quality measure through stacks of images

2-plot_GL-std_Macro is a ImageJ/Fiji macro. It measures quality through two stacks of images assumed to be acquired from two opposite angle of views using gray-level standard deviation. It is available here.