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microscopytools [2019/08/07 00:30]
bioimaging
microscopytools [2022/08/30 16:20] (current)
bioimaging [Software developed by the Bioimaging Unit]
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-<​html><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=software.png"><​BR></​html>​+<​html><​img src="/​facility/​bioimaging/​lib/​exe/​fetch.php?​media=software_neg.png"><​BR></​html>​
  
-===== Software developed by the Bioimaging ​Facility ​=====+===== 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*]]**   * {{:​icon_ubi.png?​30|}} **[[software_cclab|Cell Counter L*a*b*]]**
       * Count cells with specific nuclear and cytoplasmic staining in color images (immunohistochemical staining)       * 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]]**   * {{:​icon_ubi.png?​30|}} **[[software_mcclsm|Multichannel Cell Counter LSM]]**
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   * {{:​icon_ubi.png?​30|}} **[[software_mcc4tiff|Multichannel Cell Counter 4TIFF]]**   * {{:​icon_ubi.png?​30|}} **[[software_mcc4tiff|Multichannel Cell Counter 4TIFF]]**
       * Count cells with specific fluorescent labeling combinations - 4 TIF files       * 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 ​ ===== ===== Image analysis and visualization software ​ =====
  
-  * {{:imagej.jpg|}}  **[[http://​rsbweb.nih.gov/​ij/​|ImageJ]]**+  * {{:imagej_icon.png?35|}}  **[[http://​rsbweb.nih.gov/​ij/​|ImageJ]]**
       * The Swiss army knife of microscopy image processing       * The Swiss army knife of microscopy image processing
  
-  * {{:imagej2-icon.png?​35|}} ​ **[[http://​fiji.sc/​Fiji|Fiji]]** +  * {{:fiji-icon.png?​35|}} ​ **[[http://​fiji.sc/​Fiji|FIJI]]** 
-      * Fiji Is Just ImageJ ​(and a lot of plugins organized into a coherent menu structure)+      * 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-icon.png?​35|}} ​ **[[http://​icy.bioimageanalysis.org/​|ICY]]**
       * Icy provides the software resources to visualize, annotate and quantify bioimaging data        * Icy provides the software resources to visualize, annotate and quantify bioimaging data 
  
-  * {{::cell_profiler.png?35|}}  **[[http://​cellprofiler.org/​|CellProfiler]]**+  * {{::cellprofiler-icon.png?30|}}  **[[http://​cellprofiler.org/​|CellProfiler]]**
       * CellProfiler is free, open-source software for quantitative analysis of biological images       * CellProfiler is free, open-source software for quantitative analysis of biological images
  
 ===== Image viewers from microscopy companies ​ ===== ===== Image viewers from microscopy companies ​ =====
  
-  * {{zeiss_zen.jpg?35|}} **[[https://​www.zeiss.com/​microscopy/​int/​products/​microscope-software/​zen-lite.html|Zeiss ZEN lite for Windows]]**+  * {{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       * Supports CZI file format
  
-  * {{slidebook-icon.png?35|}} **[[https://​www.intelligent-imaging.com/​reader.php|3i Slidebook Reader]]**+  * {{slidebook_icon.png?35|}} **[[https://​www.intelligent-imaging.com/​slidebook#reader|3i Slidebook Reader]]**
       * Supports SLD file format       * 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
  
 ---- ----
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microscopytools.1565130643.txt.gz · Last modified: 2019/08/07 00:30 by bioimaging