Imaging Software
BioMedical Images
BioImage XD
www.bioimagexd.net/
BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It’s a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.
MeVisLab
www.mevislab.de/
MeVisLab represents a powerful modular framework for image processing research and development with a special focus on medical imaging. It allows fast integration and testing of new algorithms and the development of clinical application prototypes
OsiriX Medical Imaging Software
www.osirix-viewer.com/index.html
OsiriX is an image processing software dedicated to DICOM images (“.dcm” / “.DCM” extension) produced by imaging equipment (MRI, CT, PET, PET-CT, SPECT-CT, Ultrasounds, …). It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or imaging modality (C-STORE SCP/SCU, and Query/Retrieve : C-MOVE SCU/SCP, C-FIND SCU/SCP, C-GET SCU/SCP, WADO) .
VolVIEW
www.kitware.com/opensource/volview.html
VolView is an open-source, intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data on Windows, Mac and Linux computers. Users can easily load and interactively explore datasets using 2D and 3D display methods and tools. 3D tools include volume rendering, maximum intensity projections, and oblique reformatting. The ability to save an entire visualization session allows users to easily stop and start sessions. Advanced users can perform custom data processing using a simple plug-in API.
Company Free SWs
Leica Free software
LAS AF Lite
ftp://ftp.llt.de/softlib/LAS_AF_Lite/
Leica LAS AF Lite is a platform designed for advanced life science research with Leica Microsystems confocal and widefield systems. The program offers full control over the microscope hardware and at the same time minimizes the need for user interaction through intelligent automation. You can configure objectives, filter cubes and teach in parfocality and parcentricity within LAS X
Improvision Free software
VolocityLE
www.perkinelmer.com/pages/020/cellularimaging/products/volocity.xhtml
Volocity® 3D Image Analysis Software is the only solution that provides all the tools you need to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems and is fully integrated for a seamless user experience.
Nikon Free Software
Nikon EZ-C1 FreeViewer
https://www.nikon.com/products/microscope-solutions/support/download/software/confocal/c1_freevw_v390.htm
This free software package allows to view Nikon confocal images in the native ics/ids format.
SVI Free software
Huygens
https://svi.nl/FreeSfp
FreeSFP is a free of charge volume renderer that enables you to explore 3D digital images and Simulated Fluorenscence Process
Zeiss Free software
AxioVisionLE 4.5
www.zeiss.de/microscopy/de_de/home.html
Light version of Zeiss Axiovision 4.5 software can open .zvi files, owner Zeiss file format.
LSM Browser 4.2
www.zeiss.com/microscopy/en_us/downloads/lsm-5-series.html
- Image Browser, supports LSM file format
- Calculation of single 3D projections (transparency or maximum modes)
- Orthogonal Section View
- 3D Cut View
- Overlay Functionality (Scalebar, Text, Drawing functions, Time stamp, Coordinates x y z)
- Extraction of image regions
- Animation
- Color coding in Z
- Enhanced Mulltiprint with Overlay functionality
- Drag and drop of LSM images between LSM image database
ZEN Lite
www.zeiss.com/microscopy/en_us/downloads/zen.html
Use ZEN lite to:
- Control Axiocam microscope cameras
- Create microscope images and simple video sequences
- Measure distances interactively
- Manage images/videos and export them into various formats
- View meta information relating to CZI image files
- Use simple report functions
Graphics Editors
Blender
www.blender.org/
Blender is a professional free and open-source 3D computer graphics software product used for creating animated films, visual effects, art, 3D printed models, interactive 3D applications and video games. Blender’s features include 3D modeling, UV unwrapping, texturing,raster graphics editing, rigging and skinning, fluid and smoke simulation, particle simulation, soft body simulation, sculpting, animating,match moving, camera tracking, rendering, video editing and compositing. Alongside the modeling features it also has an integratedgame engine
IrfanView
www.irfanview.com/
IrfanView is a freeware/shareware image viewer for Microsoft Windows that can view, edit, and convert image files and play video/audio files. It is noted for its small size, speed, ease of use, and ability to handle a wide variety of graphic file formats, and has some image creation and painting capabilities. The software was first released in 1996. IrfanView is free for non-commercial use; commercial use requires paid registration.
The Gimp
www.gimp.org/
GIMP is an acronym for GNU Image Manipulation Program. It is a freely distributed program for such tasks as photo retouching, image composition and image authoring.
It has many capabilities. It can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc.
GIMP is expandable and extensible. It is designed to be augmented with plug-ins and extensions to do just about anything. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.
VectorMagic
vectormagic.com/home
Automatically convert bitmap images likeJPEGs, GIFs and PNGs to the crisp, clean,scalable vector art of EPS, SVG, and PDF with the world’s best auto-tracing software.
Image Analysis Processing and Rendering
Cell Profiler
cellprofiler.org/index.shtml
CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. See our papers on analyzing cell images and non-cell images
Image Surfer
imagesurfer.cs.unc.edu/
ImageSurfer is free 3D imaging software to visualize and analyze multi-channel volumes (see Feng et al. 2007 ).
Features include:
- Processing: 3D filters to improve signal-to-noise ratio.
- Restoration: deconvolution algorithms (Wiener filter, Constrained iterative, Maximum likelihood).
- Visualization: volume rendering, isosurface rendering, and a colored isosurface mode for qualitative display of the correspondence between two channels.
- Analysis and quantification: 2D slice extractor, height field display, signal intensity sampling along user defined curves.
ImageJ
rsb.info.nih.gov/ij/
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and “raw”. It supports “stacks”, a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
MIATool
www.wardoberlab.com/
The Microscopy Image Analysis Tool (MIATool) is a software application designed for the viewing and processing of large sets of image data. It makes efficient use of memory by working with pointers to images rather than the images themselves, and it saves disk space by storing reusable processing parameters in lieu of actual processed images on the hard drive. In addition, MIATool allows for multiple interpretations of a given image data set, realized by different, in general N-dimensional, arrangements of pointers to the images. A physical image data set can therefore be represented, viewed, and processed independently in different ways.
Movies Tools
VideoLan
www.videolan.org/
A project and a non-profit organization, composed of volunteers, developing and promoting free, open-source multimedia solutions.
VirtualDub
www.virtualdub.org/index.html
VirtualDub is a video capture/processing utility for 32-bit and 64-bit Windows platforms (98/ME/NT4/2000/XP/Vista/7), licensed under the GNU General Public License (GPL). It lacks the editing power of a general-purpose editor such as Adobe Premiere, but is streamlined for fast linear operations over video. It has batch-processing capabilities for processing large numbers of files and can be extended with third-party video filters. VirtualDub is mainly geared toward processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images.
Neuroimaging
Neuromantic
www.reading.ac.uk/neuromantic/
Neuromantic is a free application for the semi-manual or semi-automatic reconstruction of neurons for single images or image stacks
Neuron
www.neuron.yale.edu/neuron/
Free software for building and using computational models of neurons and networks of neurons