microscopytools
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microscopytools [2016/04/17 03:50] bioimaging created |
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.jpg"><BR></html> | + | <html><img src="/facility/bioimaging/lib/exe/fetch.php?media=software_neg.png"><BR></html> |
| - | ===== Software written by Bioimaging Facility staff ===== | + | ===== Software developed by the Bioimaging Unit ===== |
| - | * {{:icon_ubi.png?30|}} [[software_cclab|**Cell Counter L*a*b* **]] | + | * {{: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) | * Count cells with specific nuclear and cytoplasmic staining in color images (immunohistochemical staining) | ||
| - | * {{:icon_ubi.png?30|}} [[software_mcclsm|**Multichannel Cell Counter LSM**]] | + | * {{:icon_ubi.png?30|}} **[[software_cclab2|Cell Counter L*a*b* 2]]** |
| - | * Count cells with specific fluorescent labeling combinations - LSM files | + | * Count 2 different cell populations with blue and brown staining in color images (immunohistochemical staining) |
| - | * {{:icon_ubi.png?30|}} [[software_mccrgb|**Multichannel Cell Counter RGB**]] | + | * {{:icon_ubi.png?30|}} **[[software_mccczi|Multichannel Cell Counter CZI]]** |
| - | * Count cells with specific fluorescent labeling combinations - TIF files | + | * Count cells with specific fluorescent labeling combinations - CZI files |
| - | * {{:icon_staqtool.png?30|}} [[software_staqtool|**STaQTool - Spot Tracking and Quantification Tool**]] | + | * {{:icon_ubi.png?30|}} **[[software_mcclsm|Multichannel Cell Counter LSM]]** |
| - | * Track diffraction-limited spots in 2D or 3D time-lapse sequences | + | * Count cells with specific fluorescent labeling combinations - LSM files |
| - | * Quantify total fluorescence intensity with Gaussian fitting | + | |
| - | * Detect single events of fluorescence gain and loss | + | |
| + | * {{: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 ===== | ===== 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 | ||
| + | |||
| + | * {{::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 ===== | ===== 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]]** | + | * {{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|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 | ||
| ---- | ---- | ||
| [[start|Back to the Bioimaging Wiki]] | [[start|Back to the Bioimaging Wiki]] | ||
microscopytools.1460857840.txt.gz · Last modified: 2016/04/17 03:50 by bioimaging
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