Bioimaging Wiki

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===== Software written by Bioimaging Facility staff  =====

  * {{: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_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

  * {{: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

===== Image analysis and visualization software  =====

  * {{:imagej.jpg|}}  **[[http://rsbweb.nih.gov/ij/|ImageJ]]**
      * The Swiss army knife of microscopy image processing

  * {{:imagej2-icon.png?35|}}  **[[http://fiji.sc/Fiji|Fiji]]**
      * Fiji Is Just ImageJ (and a lot of plugins organized into a coherent menu structure)

  * {{icy-icon.png?35|}}  **[[http://icy.bioimageanalysis.org/|ICY]]**
      * Icy provides the software resources to visualize, annotate and quantify bioimaging data 

  * {{::cell_profiler.png?35|}}  **[[http://cellprofiler.org/|CellProfiler]]**
      * CellProfiler is free, open-source software for quantitative analysis of biological images

===== Image viewers from microscopy companies  =====

  * {{zeiss_zen.jpg?35|}} **[[http://www.zeiss.com/microscopy/en_de/downloads/zen.html#ZEN lite|Zeiss ZEN lite for Windows]]**
      * Supports CZI file format

  * {{slidebook-icon.png?35|}} **[[https://www.intelligent-imaging.com/reader.php|3i Slidebook Reader]]**
      * Supports SLD file format

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