Search Results for "microscopy"

Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools...

...Contacts: Filippo Piccinini (emails: filippo.piccinini@irst.emr.it; f.piccinini@unibo.it) Repository: https://sourceforge.net/p/colori-dt/ How to cite us when using the tool: Filippo Piccinini et al. “Colori-DT: an open-source tool for the quantitative evaluation of differences in microscopy color images”.

Analysis Nuclei DAB (AND) Tool is a Graphical User Interface (GUI) to analyse microscopy images representing cells with nuclei stained using DAB dyes. The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ...

...We analysed 217 microscopy images of untreated metaphase cells, 172 images of metaphase cells transfected with small interfering RNAs targeting the luciferase gene (as a negative control), and 230 images of metaphase cells depleted of CHC. Using the quantified data, we trained 23 supervised machine learning classificatio

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

...(XMIPP is a suite of image processing programs primarily aimed at obtaining the three-dimensional reconstruction of biological specimens from projection images obtained by transmission electron microscopy)