A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Dec 20, 2010



ImageJ is a public domain Java image processing program. 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.
It canbe used in scientific research to calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.
Website to Download: http://rsbweb.nih.gov/ij/download.html

GelAnalyzer is a 1D gel electrophoresis image analysis software available freely for educational institutes, researchers, and small companies. Main features of  Gelanalyzer includes improved automatic lane detection, automatic band detection, background subtraction techniques: Rolling ball, valley to valley, manual baseline.
Rf calibration to repair gel run distortions, accurate quantity and molecular weight calculations with 4 different calibration curve types. The process of gel image analysis is straightforward and covers all the main aspects of evaluation from automatic lane detection to precise molecular weight calculations. Many tools help you to improve the accuracy of gel evaluation, such as background subtraction methods and Rf calibration. These features make GelAnalyzer a real solution to gel image analysis in cost sensitive enviroments.

Volocity Demo

A feature-filled, user friendly software product, provided free of charge to researchers. Volocity is the universal solution for 3D analysis of fluorescence microscopy images.A collection of high performance 3D imaging software products, Volocity lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication.Once you have downloaded Volocity Demo it is free for you to use for as long as you like.  There is no time limit or trial period. 


Automated image analysis software, CellC, was developed and validated for quantification of bacterial cells from digital microscope images. CellC enables automated enumeration of bacterial cells, comparison of total count and specific count images [e.g., 4′,6-diamino-2-phenylindole (DAPI) and fluorescence in situ hybridization (FISH) images], and provides quantitative estimates of cell morphology. The software includes an intuitive graphical user interface that enables easy usage as well as sequential analysis of multiple images without user intervention.


TMAJ is open-source software designed to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.

VisBio 3.00

VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data.

Website to download: http://www.loci.wisc.edu/visbio/downloads

Scion Image

Scion Image for Windows is the Windows version of Scion Image, which is in turn a version of the popular Macintosh program, NIH Image, written at the National Institutes of Health. Scion Image may be used to capture, display, analyze, enhance, measure, annotate, and output images. Scion Image extensively supports Scion CG-7, LG-3, VG-5 and AG-5 frame grabber boards, and provides a powerful and complete image acquisition environment.

Scion Image for Windows supports color and grayscale image capture with Scion frame grabbers. It includes advanced capturing capabilities such as frame averaging and summation, frame sequence capture, and on-chip integration support. All current features of NIH Image have been included.

Website to download:

GetData Graph Digitizer

GetData Graph Digitizer is a program for digitizing graphs and plots. It is often necessary to obtain original (x,y) data from graphs, e.g. from scanned scientific plots, when data values are not available. GetData Graph Digitizer allows to easily get the numbers in such cases.

Welcome to the home page of freeware TLC and gel analysis software CP ATLAS 2.0! CP ATLAS is the ideal choice for students, teachers, schools, colleges, universities and even for smaller companies to analyze TLC and gel images. With CP ATLAS you don't need a professional densitometer for simple quantitative analysis. You can use a simple digital camera, office scanner or mobile phone to get a picture. With CP ATLAS the analysis takes only a few seconds, and you can copy the results to your spreadsheet software for further usage. CP ATLAS is an easy-to-use computer program that combines 25 years of professional experience with the power of modern computer programming. It's a cross platform software written in Java language, thus it runs on any computer, which has Java Runtime Environment (JRE) installed on