PatternUnmixer (formerly called PUnmix) learns a model of fundamental subcellular patterns using user-specified images of “pure” subcellular patterns (e.g., lysosomes, endosomes) and then uses that model to calculate the fraction of probe in each subcellular compartment for images containing mixed patterns.
HypoTrace takes time series of image files as input and output growth rate as well as hook angle measurements for Hypocotyls. The software comes with a build-in Graphical User Interface, which allows the software to be run under three modes: 1. Automatic mode with no user intervention, good for high quality images; 2. Semi-Auto mode with a little bit user intervention, good for fair quality images; 3. Manual mode, work for all images including really bad quality images. The three modes are designed to effectively detect the cotyledons bifurcation point under all conditions.
Engauge Digitizer converts an image file showing a graph or map, into numbers. The image file can come from a scanner, digital camera or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet.
CI Micro was developed primary for quickly analyzing time-lapse experiments of cell migration, invasion and wound healing assays. Time-lapse experiments saved in Leica’s LIF or (auto-saved) XLEF files can be opened with no delay in loading time. Interactive measurements can be done by the area or counting tool and are save together with experimental data. Extra options are Movie Export, 3D features and support for TIFF files.
Graf J, Cho S, McDonough E, Corwin A, Sood A, Lindner A, Salvucci M, Stachtea X, Van Schaeybroeck S, Dunne PD, Laurent-Puig P, Longley D, Prehn JHM, Ginty F. FLINO-A new method for immunofluorescence bioimage normalization.
Bioinformatics. 2021 Oct 2:btab686. doi: 10.1093/bioinformatics/btab686. Epub ahead of print. PMID: 34601553.