Other useful tools
AMF
An adaptive filter for confocal-type microscopy to remove isolated pixels. Confocal-type images often exhibit isolated pixels (1×1 ~ 5×5) with extremely bright values caused by voltage instability or dead or hot pixels. The magnitudes of these pixels are approximately 5 to 100 times higher than the normal intensity amplitudes of the biostructure. These isolated pixels are unsuitable for subsequent analysis or processing.
Java ImageJ-plugin
t-varianceJ
A simple FIJI/ImageJ plugin for t-axial variance calculation assisting in calcium signal profiling. It will highlight the regions that have calcium signal transients.
Java ImageJ-plugin
Palette
Merge channels: A tool for multi-color 2D or 3D imaging. This tool can adjust the 4 color channel components (RGB), the GAIN (the brightness to display) and also the gamma (adjust the histogram to make images more 'naturally').
MATLAB
Simulation for adaptive optics
Simulation for sensorless adaptive optics (Confocal microscopy, Modal method). The simulation generates the aberrated PSF on the pupil with Zernike polynomial 5-22 orders, and corrects them with different method.
MATLAB