===== Software developed by the Bioimaging Unit ===== * {{:icon_staqtool.png?30|}} **[[software_staqtool|STaQTool - Spot Tracking and Quantification Tool]]** * Track diffraction-limited spots in 2D or 3D time-lapse sequences * Quantify total fluorescence intensity with Gaussian fitting * Detect single events of fluorescence gain and loss * {{:icon_ubi.png?30|}} **[[software_cclab|Cell Counter L*a*b*]]** * Count cells with specific nuclear and cytoplasmic staining in color images (immunohistochemical staining) * {{:icon_ubi.png?30|}} **[[software_cclab2|Cell Counter L*a*b* 2]]**  * Count 2 different cell populations with blue and brown staining in color images (immunohistochemical staining) * {{:icon_ubi.png?30|}} **[[software_mccczi|Multichannel Cell Counter CZI]]** * Count cells with specific fluorescent labeling combinations - CZI files * {{:icon_ubi.png?30|}} **[[software_mcclsm|Multichannel Cell Counter LSM]]** * Count cells with specific fluorescent labeling combinations - LSM files * {{:icon_ubi.png?30|}} **[[software_mccrgb|Multichannel Cell Counter RGB]]** * Count cells with specific fluorescent labeling combinations - RGB TIF files * {{:icon_ubi.png?30|}} **[[software_mcc4tiff|Multichannel Cell Counter 4TIFF]]** * Count cells with specific fluorescent labeling combinations - 4 TIF files ===== Image analysis and visualization software ===== * {{:imagej_icon.png?35|}} **[[http://rsbweb.nih.gov/ij/|ImageJ]]** * The Swiss army knife of microscopy image processing * {{:fiji-icon.png?35|}} **[[http://fiji.sc/Fiji|FIJI]]** * Fiji Is Just ImageJ focused on the visualization and analysis of microscope images in 2D, 3D, 4D and 5D * {{icy-icon.png?35|}} **[[http://icy.bioimageanalysis.org/|ICY]]** * Icy provides the software resources to visualize, annotate and quantify bioimaging data * {{::cellprofiler-icon.png?30|}} **[[http://cellprofiler.org/|CellProfiler]]** * CellProfiler is free, open-source software for quantitative analysis of biological images ===== Image viewers from microscopy companies ===== * {{zen_icon.png?35|}} **[[https://www.zeiss.com/microscopy/int/products/microscope-software/zen-lite.html|Zeiss ZEN lite for Windows]]** * Supports CZI file format * {{slidebook_icon.png?35|}} **[[https://www.intelligent-imaging.com/slidebook#reader|3i Slidebook Reader]]** * Supports SLD file format * {{::las_x.png?35|}} **[[https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/|LAS X Core]]** * Supports LIF file format * {{::imaris_logo.png?35|}} **[[https://imaris.oxinst.com/imaris-viewer|Imaris Viewer]]** * For viewing raw images as well as those analyzed within Imaris ---- [[start|Back to the Bioimaging Wiki]]