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


Free, ImageJ plus a large bundle of plugins, in one easy-to-download application including utilities for 3D viewing, video editing, measuring colocalization. 


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



Free, Relion is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination


Charged, PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger


Free, A comprehensive software package for macromolecular structure determination using crystallographic and electron cryo-microscopy data


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


Free, EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes


Free, CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines


Free, Crystallographic Object-Oriented Toolkit


Charged, Based on the principle of tomography, 3D reconstruction is carried out simply and quickly from continuous tilt images taken by TEM



Charged, A programming and computing platform that used for MR imaging processing


Free, MRI viewer and a programme to convert between different image files (e.g., dicom to nifti)


Free, An open-source toolbox for analysing anatomical and functional neuroimaging