Analysis
Programs that can view or analyze images. We will also offer our own image quality assessment program.
Optical Images
Zeiss ZEN lite
Free, software from Zeiss to open .czi files. It can perform image acquisition or fundamental image analysis and processing tasks
NIS-Elements Viewer
Free, imaging sofware from Nikon for viewing microscopy image files and datasets
LAS X Core
Free, software from Leica to open images acquired on the Leica SP8 confocal or any microscope controlled by LAS X
IMARIS viewer
Free, Imaris Viewer with limited capabilities is a free 3D/4D microscopy image viewer for viewing raw images as well as those analyzed within Imaris
Fiji
Free, ImageJ plus a large bundle of plugins, in one easy-to-download application including utilities for 3D viewing, video editing, measuring colocalization.
Celleste
Charged, Image analysis software from ThermoFisher Scientific compatible with EVOS cell imaging system
Cell Profiler
Free, open-source software from the Broad Institute for segmentation and quantitative analysis of microscope image data
EM
RELION
Free, Relion is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination
pymol
Charged, PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger
phenix
Free, A comprehensive software package for macromolecular structure determination using crystallographic and electron cryo-microscopy data
IMOD
Free, A set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections
eman2
Free, EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes
CryoSPARC
Free, CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines
coot
Free, Crystallographic Object-Oriented Toolkit
Composer-Temography
Charged, Based on the principle of tomography, 3D reconstruction is carried out simply and quickly from continuous tilt images taken by TEM
MR
MATLAB
Charged, A programming and computing platform that used for MR imaging processing
MRICron
Free, MRI viewer and a programme to convert between different image files (e.g., dicom to nifti)
FreeSurfer
Free, An open-source toolbox for analysing anatomical and functional neuroimaging