Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.
Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.
An ImageJ macro for correcting frame drift occurred during image acquisition.
It often happens that you have an image sequence that shows problematic drifting of image frame and at the same time you have some landmarks that could be used for correcting the drift. This ImageJ macro allows you to Manually track the landmark using ImageJ Manual Tracking Plugin. Using the coordinates recorded in the Result window, each frame is shifted back so that the landmark stays in a single place.
Three different methods for correcting fluorescence bleaching.
1. Simple (framewise ratio based)
2. Exponential (curve fitting with exponential decay model)
3. Histogram matching (register histogram shape. with 16 bit, it takes long time... it should be improved).
This plugin can be used to estimate nonlinear distortions induced by the image acquisition process . It does not require special calibration samples, but needs sufficient overlapping image areas with preferably high contrast. For further information on how to best arrange calibration images please see the documentation.