Luiz Guilherme Garcia Greca

Open source software packages are made possible mainly through the GNU
General Public License. It basically uses the principle that people must have the
freedom to share and change any software under this license, in a way that
everyone can have access and benefit from constant developments and
improvements. For that reason, mainly, such software licenses are widely used
when it comes to specialized applications. Research institutes, universities,
movie makers, industry, governmental agencies and the people sharing
hobbies that depend on good software packages are all good examples of very
common and demanding users who also contribute with improvements in an
extensive way.
Among those afore mentioned specialized applications, the fields of
microscopy, image analysis, image processing and ccd-camera control have
innumerous open source software packages and free websites that offer
practically all the same tools than commercial alternatives. From a quick search
in on the Free Software Foundation directory, it is possible to come up with tens
of possibilities. A few of them are:
EMAN ( http://www.msg.ucsf.edu/local/programs/eman/ )
EMAN is a suite of scientific image processing tools aimed primarily at the
transmission electron microscopy community, though it is beginning to be used
in other fields as well. EMAN has a particular focus on performing a task known
as single particle reconstruction. In this method, images of nanoscale
molecules and molecular assemblies embedded in vitreous (glassy) ice are
collected on a transmission electron microscope, then processed using EMAN to
produce a complete 3-D recosntruction at resolutions now approaching atomic
resolution. For low resolution structures (~2 nm), this may require ~8 hours of
computer processing and a few thousand particles. For structures aimed at
~0.5 nm or better resolution, hundreds of thousands of particles and hundreds
of thousands of CPU-hours (on large computational clusters) may be required.
Indeed, EMAN is often used in supercomputing facilities as a test application for
large-scale computing.
Gwyddion ( http://gwyddion.net/ )
Gwyddion is a modular SPM (Scanning Probe Microsope) data visualization and
analysis tool. It can be used for all most frequently used data processing
operations including: leveling, false color plotting, shading, filtering, denoising,
data editing, integral transforms, grain analysis, profile extraction, fractal
analysis, and many more. The program is primarily focused on SPM data
analysis (e.g. data obtained from AFM, STM, NSOM, and similar microscopes).
However, it can also be used for analyzing SEM (scaning electron microscopy)
data or any other 2D data."

BioImageXD (http://www.bioimagexd.org/)
BioImageXD is a free open source software package for analyzing, processing
and visualizing multi-dimensional microscopy images.[] BioImageXD is a
multi-purpose post-processing tool for bioimaging. The software can be used
for simple visualization of multi-channel temporal image stacks to complex 3D
rendering of multiple channels at once. Animations of 3D renderings can be
easily created using virtual camera flying paths or key-frames. Image
processing tools include deconvolution, registration and tens of tools for
mathematical and logical processing and noise reduction. Analysis tools cover
both object-based and voxel-based approaches, with for instance versatile tools
for colocalization analysis, numerous segmentation methods with elaborate
numerical analyses, and an advanced motion tracking algorithm. All processing
and analysis methods can be built into pipelines and run for hundreds of
datasets at once with the Batch Processor, and simulated image data can be
created for method validation. BioImageXD features an intuitive graphical user
interface, designed to enable accurate scientific quality and control, and image
processing in high throughput.
Micro-Manager ( http://www.ccd.com/software.html )
(Plug-in
running
under
ImageJ
for
microscope
automation)
Micro-Manager software runs under ImageJ to provide control of automated
microscopes, supporting time-lapses, multi-channel imaging, z-stacks, and
combinations thereof. Micro-Manager works with microscopes from all four
major manufacturers (Leica, Nikon, Olympus and Zeiss), and peripherals such
as stages, filter wheels, and shutters.
KestrelSpec ( http://www.ccd.com/software.html )
KestrelSpec for Windows from Catalina Scientific is real-time imaging
spectroscopy software that has the same look and functionality as Rhea
Corporation's KestrelTM software for the Macintosh. KestrelSpec is designed for
data acquisition, data display and analysis for Raman, fluorescence and
UV/visible spectra.
If not stated, all mentioned software packages are compatible with Windows
and UNIX like systems.
These are only few examples of the kind of software that is freely available for
microscopy and other lab uses. But the most important of all is to be aware of
the existence of such handy and freely available tools.