OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

Abstract

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

ColonyCountJ: A User-Friendly Image J Add-on Program for Quantification of Different Colony Parameters in Clonogenic Assay

“…To overcome the manual counting problems, several semiautomated and automated colony counters have been designed [2][3][4][5][6] and each has certain limitations. Here we have developed a userfriendly and semi-automatic program for gathering colony parameters in clonogenic assay.…”

“…To overcome these key issues associated with the manual counting, automated colony counters have been designed which offer faster and more reproducible results which can be automatically transferred onto a computer. Many groups have developed automatic colony counting methods based on the image analysis principles [2][3][4][5][6], but they have either used commercial software or their uses require in-depth knowledge of computer programming skills. Several colony counting instruments are commercially available, but they are not cost effective.…”

“…Most of the automatic colony counters that are commercially available use CCD-camera and specialized imaging software. Free colony counting softwares such as Clono-Counter [3][4][5], ColonyArea [6] are available; however, there are certain drawbacks such as non-availability of quantitative guidelines on how to select key digital counting parameters such as intensity threshold and colony size. Therefore, still manual counting method is adapted by many researchers for studies involving clonogenic assays as the standard procedure [1,7,8].…”

ESTIMATING NUMBERS OF OIL PALM (Elaeis guineensis) POLLEN GRAINS USING IMAGE ANALYSIS AND PROCESSING

“…Debris might form clusters with pollen which make it difficult for software to delineate individual pollen to give a correct count (Mudd and Arathi, 2012). However, for many biological studies involving counting of small biological particle, a moderate deviation (lower than 20%) is often negligible compared to noise generated by other factors (Geissman, 2013). Yet, further studies are needed to: (1) improve method for separation of pollen from debris, (2) improve sensitivity of the pollen detection program, allowing for a better understanding of pollination process in oil palm, and (3) further application of this software to counting small circular objects in oil palm research (i.e.…”

“…One possibility is to use an image processing tool and analysis program which offer a more accurate, user friendly, and consistent estimation (Bechar et al, 1997;Aronne et al, 2001;Fonseca et al, 2002;Costa and Yang, 2009;Geissman et al, 2013;Mudd and Arathi, 2012). This tool is equipped with a particular computer software to scan pollen images, which previously captured as raw images by a camera.…”