1 - 17 of 17 results


A Java library facilitating bi-directional interoperability between MATLAB and ImageJ applications. ImageJ-MATLAB provides an extensible and bidirectional bridge for mutual exchange of data between these two environments. The foundation of ImageJ-MATLAB consists of two Converter plugins: enabling ImageJ Datasets and MATLAB matrices to be freely exchanged within the SciJava framework. Both directions of conversion use the third-party MATLABControl library to manage interaction with a MATLAB instance.


Analyses data in the context of dithionite scramblase assays. flippant allows to analyze data from statistical computing and graphics and arrives at publication-grade graphics that offer extensive facilities for individual optimization and adaptation. It provides a platform for review, dissemination and extension of the strategies it employs. The tool was tested by reanalyzing a subset of data. It shows identical trends and close matches of the results, supporting identical conclusions.

SC-QI / Structural Contrast-Quality Index

Explores effective features that are consistent with the characteristics of a human visual system (HVS) for visual quality perception. Image quality assessment (IQA) is a computational method that adoptes a structural contrast index (SCI), which can well characterize local and global visual quality perceptions for various image characteristics with structural-distortion types. It tends to adaptively characterize perceived visual quality for different image texture characteristics with structural-distortions types where the structural-distortion is defined as a distortion due to change in inter dependency among neighbour pixels.

Biosensor Processing

Allows processing raw ratiometric biosensor images into fully corrected "ratio maps" or "activation maps” - images. Biosensor Processing includes, for quantitative widefield imaging of ratiometric biosensors, application of all necessary image corrections needed. This tool follows a 6-steps procedure: (i) shading correction; (ii) background subtraction; (iii) image masking; (iv) automated image registration; (v) image shear, rotation and scaling correction; and (vi) ratio calculation.

CGE / Circadian Gene Expression

Automatically tracks moving cells over longer period of time. CGE consists of two ImageJ plugins: (1) CGE_Preprocessor that precomputes all data required for the recording, and (2) CGE_Recorder that uses the data produced by the first plugin and interacts with the user to determine the trajectory and the outline of a nucleus. The software allows one to study the different features and changes of cells with significantly varying locations and protein expression levels imaged over a period of several days.

SAFA / Semi-Automated Footprinting Analysis

Allows quantification of a footprinting gel. SAFA contains a graphical user interface (GUI) that guides users through the analysis to generate the numerical output of the band intensities. This tool automates all the steps involved in gel analysis. It permits the visualization of the results of the automated procedure at each step, and the automated correction of geometric distortions in the gel. In summary, it’s a tool to pursue the quantitative information that is inherent to designed footprinting experiments.