• 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

• Cell Counter L*a*b*
  • Count cells with specific nuclear and cytoplasmic staining in color images (immunohistochemical staining)

• Cell Counter L*a*b* 2 
  • Count 2 different cell populations with blue and brown staining in color images (immunohistochemical staining)

• Multichannel Cell Counter CZI
  • Count cells with specific fluorescent labeling combinations - CZI files

• Multichannel Cell Counter LSM
  • Count cells with specific fluorescent labeling combinations - LSM files

• Multichannel Cell Counter RGB
  • Count cells with specific fluorescent labeling combinations - RGB TIF files

• Multichannel Cell Counter 4TIFF
  • Count cells with specific fluorescent labeling combinations - 4 TIF files

• ImageJ
  • The Swiss army knife of microscopy image processing

• FIJI
  • Fiji Is Just ImageJ focused on the visualization and analysis of microscope images in 2D, 3D, 4D and 5D

• ICY
  • Icy provides the software resources to visualize, annotate and quantify bioimaging data

• CellProfiler
  • CellProfiler is free, open-source software for quantitative analysis of biological images

• Zeiss ZEN lite for Windows
  • Supports CZI file format

• 3i Slidebook Reader
  • Supports SLD file format

• LAS X Core
  • Supports LIF file format

• Imaris Viewer
  • For viewing raw images as well as those analyzed within Imaris

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