Fluorescence microscopy

Particle detection is based on "Analyze Particles" in ImageJ. It probably could also be used in spot detection, not limited to centromere. >This macro is described in Bodor et al. (2012). The macro recognizes centromere or kinetochore foci in Delta Vision or TIFF images and determines their centroid position. Fluorescent intensities are then measured for each centromere by placing a small box around the centroid position of the centromere. The peak intensity value within the box is corrected for local background by subtraction of the minimum pixel value. This process results in an accurate measurement of large numbers of centromere or kinetochore-specific signals. Following papers uses CRaQ (picked up, maybe more): - Fachinetti et al. (2017), Developmental Cell 40, 104–113, - Guo et al. (2017) Nature Communications volume 8, Article number: 15775 (2017) doi:10.1038/ncomms15775 - Lgosdon et. al. (2015) J Cell Biol Mar 2015, 208 (5) 521-531; DOI: 10.1083/jcb.201412011 - Bodor et al. (2014), eLife. 2014; 3: e02137

The Huygens Software Suite consists of different image processing packages with functionalities that include deconvolution, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as widefield, confocal, multi-photon, spinning disk, Array Detector, STED, and Light Sheet

Deconvolution software

Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.