plugin

Rigid registration of time series in 3D. A video tutorial is available (be careful of sounds, the video automatically starts!): [Sample Drift Correction Following 4D Confocal Time-lapse Imaging](http://www.jove.com/video/51086/sample-drift-correction-following-4d-co…)

ImageJ plugin to analyze changes in vessel diameters, described in Fernández er al (2014). More specifically the paper describes the measurement of isolated retinal arterioles (ca 50 micrometer diameter) but can be used for diameter measurements of similar vessel structures.

Variational algorithms to remove stationary noise. Application to microscopy imaging. This plugin allows to denoise images degraded with stationary noise. Stationary noise can be seen as a generalization of the standard white noise. Typical applications of this plugin are:

- Standard white noise denoising using a total variation and fidelity term minimization. Even though total variation denoising is not the state of the art (regarding SNR improvement), it may be very valuable for further tasks such as image seg- mentation).

- Destriping (the problem that motivated us to develop these ideas). 

- Deconvolution (even though most users won't be able to use this feature).

- Cartoon + texture decomposition which might be useful to compress images, analyse textures or simplify segmentation like tasks.

A Jython script using the plugin : Register Virtual Stack Slices It takes a sequence of image slices stored in a folder, and delivers a list of registered image slices (with enlarged canvas). One of the images in the sequence can be selected by the user as reference and it will remain intact. The plugin can perform 6 types of image registration techniques: - Translation - Rigid (translation + rotation) - Similarity (translation + rotation + isotropic scaling) - Affine - Elastic (via bUnwarpJ with cubic B-splines) - Moving least squares All models are aided by automatically extracted SIFT features.

This plugin will return on a full 256-grey level image (limitation in this version) or on a ROI several texture features such as described in Haralick publication. Can be run in batch mode.