Evaluation of an Automated Colony Counter

An automated colony counter was found to readily detect surface and subsurface bacterial colonies of 0.3-mm size or greater with a high degree of precision. On a logarithmic scale, counting efficiency consistently ranged from 89 to 95% of corresponding manual count determinations for plates containing up to 1,000 colonies. In routine application, however, automated plate counts up to approximately 400 colonies were selected as a more practical range for operation. The automated counter was easily interfaced with an automated data acquisition system.     

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays.     

Increased salt- and nisin-sensitivity of pressure-injured bioluminescent Listeria monocytogenes

Suspensions of a bioluminescent (luxAB) transformant of Listeria monocytogenes in pH 7.0 phosphate buffer were pressurised and the effect of the pressure treatment was monitored by plate counting. When the bacteria were suspended in NaCl- and nisin-free buffer the number of colony forming units (CFU) decreased by 3 and 6 log cycles after 300 MPA for 10 and 30 min, respectively. Supplementing the plating medium with 5% NaCl did not influence the colony forming capacity of non-pressurised cells, however, CFU of residual populations after respective treatments of 300 MPa for 10 and 30 min were reduced by a further 2 and 3.5 log cycles in case of salt containing plates. Nisin-addition to the plating medium caused less than one log unit decrease in the CFU of the non-pressurised population. However, the CFU of 10 min-pressurised sample was 4 log cycles less in the nisin-containing plates than in the nisin-free ones, whereas no colonies were formed in the nisin-containing plates even when 1 ml was inoculated from the originally 10(10) CFU/ml population after 300 MPa for 30 min. The luciferase activities (bioluminescence intensities) decreased concomitant with the reduction of the viable cell counts, however, they were approx. 0.6-0.8 log units less in the presence of 5% NaCl in the pressurised suspension than those expected from the previously established linear correlation between the logarithmic light outputs and the logarithmic viable cell counts.     

Automated counting of bacterial colony forming units on agar plates

Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates.A colony counter hardware was designed and a novel segmentation algorithm was written in MATLAB. In brief, pre-processing with Top-Hat-filtering to obtain a uniform background was followed by the segmentation step, during which the colony images were extracted from the blood agar and individual colonies were separated. A Bayes classifier was then applied to count the final number of bacterial colonies as some of the colonies could still be concatenated to form larger groups. To assess accuracy and performance of the colony counter, we tested automated colony counting of different agar plates with known CFU numbers of S. pneumoniae, P. aeruginosa and M. catarrhalis and showed excellent performance.     

Automated counting of human tumour colonies in the Courtenay-Mills assay system

A procedure for using the Omnicon automated image analysis system for counting colonies grown from a human tumour cell line (COLO 205) in the Courtenay-Mills assay is described. This involves the transfer of the agar medium from culture tubes into petri dishes. Comparisons of observer and instrument counts were done on a blinded basis. Run-to-run correlation coefficient was 0.996 for automated counting and the inter-observer correlation coefficient was 0.984. Both assessments showed a linear relationship between the number of cells plated and the number of colonies grown. Automated colony counting is fast, reliable and provides additional information on colony size distribution, not obtainable with manual counting. This automated procedure will greatly facilitate in vitro drug sensitivity evaluation.     

TEMPERATURE-DEPENDENT CHANGES IN COLONY SIZE OF THE FRESHWATER PENNATE DIATOM ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE) AND THEIR POSSIBLE ECOLOGICAL IMPLICATIONS1

Changes in colony size (cell number per colony) of Asterionella Formosa Hass. were experimentally evaluated in relation to water temperature using two types of clones having colony sizes of four or eight cells. The clones were isolated from two different temperate freshwater lakes. Both clones showed the same general trend with changing temperature. Most of the colonies were normal in size at low temperatures, but colony size was twice as large at high temperatures. Variable colony sizes were present at low percentages. Colony separation occurred at the oldest connection within the colony after cell division. Culture experiments showed that the rates of specific growth and colony separation were balanced except for a rather short period of time when the temperature was changed. Optical and scanning electron micrography did not show any distinctive morphological structure at the point of connection except for porelli and mucilage pads. Seasonal changes in colony size of A. formosa observed in a freshwater lake are discussed based on these temperature results.     

The effect of sodium chloride concentration and pH on the growth of Salmonella typhimurium colonies on solid medium

The growth of Salmonella typhimurium colonies on a model food system (agar solidified culture medium) was followed. Colony radius, determined using computer image analysis (IA) techniques, and viable cell number per colony were measured as indices of colony growth, and the effect of [NaCl] (0.5–3.5% (w/v)) and pH (7.0–5.0) on colony growth at 30°C was observed; colonies were point inoculated from serial dilutions. Colony growth (between 13 and 26 h after inoculation) was linear when expressed in terms of radius, and exponential when expressed in terms of viable cell number per colony. Overall, both increasing the [NaCl] and decreasing the pH had little effect on colony growth, other than to delay the onset of linear radial growth. Initial specific growth rate (μ) ranged from 0.73 to 0.87 h⁻¹. Thin films of agar medium on microscope slides allowed the growth of microcolonies to be observed after just 4 h incubation. A greater understanding of the growth kinetics of bacterial colonies, and the effects of environment on such data, may enable better control of foodborne bacterial pathogens, and consequently an improvement in food product safety.     

Sampling efficacy for the red imported fire ant Solenopsis invicta (Hymenoptera: Formicidae)

Cost-effective detection of invasive ant colonies before establishment in new ranges is imperative for the protection of national borders and reducing their global impact. We examined the sampling efficiency of food-baits and pitfall traps (baited and nonbaited) in detecting isolated red imported fire ant (Solenopsis invicta Buren) nests in multiple environments in Gainesville, FL. Fire ants demonstrated a significantly higher preference for a mixed protein food type (hotdog or ground meat combined with sweet peanut butter) than for the sugar or water baits offered. Foraging distance success was a function of colony size, detection trap used, and surveillance duration. Colony gyne number did not influence detection success. Workers from small nests (0- to 15-cm mound diameter) traveled no >3 m to a food source, whereas large colonies (>30-cm mound diameter) traveled up to 17 m. Baited pitfall traps performed best at detecting incipient ant colonies followed by nonbaited pitfall traps then food baits, whereas food baits performed well when trying to detect large colonies. These results were used to create an interactive model in Microsoft Excel, whereby surveillance managers can alter trap type, density, and duration parameters to estimate the probability of detecting specified or unknown S. invicta colony sizes. This model will support decision makers who need to balance the sampling cost and risk of failure to detect fire ant colonies.     

Evaluation of an Automatic Electronic Device for Counting Bacterial Colonies

An automatic colony counter was tested extensively with colonies of two bacterial species, Serratia marcescens and Bacillus subtilis var. niger, grown on agar media. A stable relationship was established between machine counts and counts done visually by technicians. The calibration curve and estimates of the efficiency of the machine are presented and discussed. It is estimated that a 40% reduction in colony counting time is feasible through use of the machine.     

COLONY FORMATION IN AGAR: IN VITRO ASSAY FOR HAEMOPOIETIC STEM CELLS

Using a method in which embryo fibroblasts were used as feeder layers, the colony forming capacity in agar of a variety of mouse haemopoietic suspensions was compared with their CFU s content. A striking parallelism between the results of the two assays was found. In addition, under certain conditions higher numbers of CFU s could be retrieved from 5-day-old agar colonies than were originally plated, indicating that the CFC a (Colony Forming Cell agar) may fulfil the requirements of pluripotency as well as of self-renewal, both prerequisites for any haemopoietic stem cell candidate. Although our data by no means provide direct proof that the CFC s and the CFC a are identical, they certainly support such a concept. the contradictory findings by others that CFU s and CFU c (Colony Forming Unit culture) can be separated on a velocity gradient is attributed to different culture conditions, in other words, that their CFU cè are not identical with our CFU a .
Our findings also indicate that for mouse cells our soft agar colony assay meets the criteria of a quantitative assay for haemopoietic stem cells and that extension of this technique to bone marrow of primates including humans seems to be justified.     

Effects of colony size on larval performance in a processionary moth

1. Some lepidopteran species have larvae that live gregariously, especially in early instars. Colony‐living species may benefit from improved protection from predators, thermoregulation, and feeding facilitation, for example. 2. While many studies have compared solitary and gregarious life styles, few data exist as to the relationship between size of the larval colony and larval performance in gregarious species. The present study was aimed at understanding the importance of colony size for growth and survival of the northern pine processionary moth (Thaumetopoea pinivora) larvae. 3. Field studies, comparing three different sizes of colonies of T. pinivora larvae, showed that individuals in larger colonies had a higher survival rate compared with those living in smaller colonies and also a faster growth rate. 4. The higher survival rate of large colonies was attributed to improved protection from predacious arthropods. 5. In early spring, the young larvae bask in the sun to increase their body temperature. In field experiments the thermal gain was higher in large colonies, and individuals in such colonies also grew faster. As growth rate was not affected by colony size when the ability to bask was experimentally removed in a laboratory experiment, the higher growth rate of the larger colonies was probably due to improved thermoregulation rather than feeding facilitation. 6. The size of larval colonies of gregarious insects depends on natural mortality events as well as on female oviposition strategy. Our results show that decreasing colony size can lead to a reduction in growth rate and survival. It is therefore important to understand whether or not small colonies will benefit equally from the gregarious behaviour.     

Growth-related changes in predation behavior in incipient colonies of the ponerine antEctatomma tuberculatum (Olivier)

Summary We traced the development in the laboratory of 18 young colonies of the arboricolous ponerine antEctatomma tuberculatum. Colony foundation is of the partially-claustral type. During the early stages, when the colony is entirely dependent on the queen's behavior, the growth of the colony in terms of number of workers produced over time was relatively predictable. Afterwards, divergence in colony growth in function of the time increases as fast as the number of workers influences the efficiency of colony provisioning.Comparative analysis indicated clear changes in the predation behavior of foundresses and workers as colonies developed. For any stage of colony growth, all individuals provisioned the nest with dead prey or sugar-rich substances in the same way. However, prey hunting involves two different strategies. Foundresses and nanitic workers (originating from colonies with 9–15 workers) foraged actively, catching prey as the result of random encounters. Post-nanitic foragers (originating from colonies with 20–30 workers) and those from nature colonies developed an ambush strategy. Workers in these colonies gained experience at catching and handling prey during a period when they acted as nest guards, and so tended to be more efficient hunters than poorly experienced foundresses or nanitic foragers. The change in strategy was also positively correlated with an increase in the size of workers as the colony matured. A stable maximum in workers size is apparently reached only after the appearance of efficiently hunting foragers, presumably in numbers sufficient to provide adequate quantity and quality of larval food. Such a correlation between worker size and colony growth, assumed general for all ants, has not been demonstrated for Ponerinae before this work.     

Enumeration of heterotrophs, fecal coliforms and Escherichia coli in water: comparison of 3M Petrifilm plates with standard plating procedures

A total of 177 naturally contaminated water samples were analyzed by membrane filtration according to the Standard Methods for the Examination of Water and Wastewater published by the American Public Health Association. Filters were incubated in parallel on mHPC-agar and 3M™ Petrifilm™ Aerobic Count Plates (Petrifilm™ AC plates) for heterotrophic counts. Fecal coliforms and Escherichia coli were enumerated on mFC-agar and 3M™ Petrifilm™ E. coli/Coliform Count Plates (Petrifilm™ EC plates). Typical colonies on each media type were confirmed following standard procedures. Heterotrophic counts were between 10³ and 10⁴ CFU/mL and the average log₁₀ counts obtained on Petrifilm™ AC plates were about two-fold lower than on mHPC-agar. Counts for fecal coliforms and E. coli were between 10² and 10³ CFU/mL. Average log₁₀ counts for confirmed fecal coliforms obtained on Petrifilm™ EC plates were slightly lower than on mFC agar with a correlation coefficient of 0.949. The average log₁₀ counts for confirmed E. coli on Petrifilm™ EC plates and on mFC agar were statistically not different (P=0.126) with a correlation coefficient of 0.879. Specificity of Petrifilm™ EC plates and mFC agar was evaluated by comparing typical colony counts with confirmed counts. On mFC agar, counts for typical colonies were by 2 log₁₀ CFU higher than the actual confirmed counts. In contrast, on Petrifilm™ EC plates typical colony counts were almost identical to confirmed colony counts for both fecal coliforms and E. coli. This comparison illustrates the high specificity of Petrifilm™ EC plates for enumeration of both fecal coliforms and E. coli in water.     

Specificity of grouping behaviour: comparing colony sizes for the same seabird species in distant populations

Animal collective patterns such as group size frequency distributions often show substantial intraspecific variation, suggesting low species‐specific consistency. Here, we dissect intraspecific vs interspecific components of colony size variation to estimate the repeatability (R) of colony size frequency distribution (CSFD) statistics for seabird species breeding in at least two out of four distant geographic areas of the Northern Hemisphere (21 species; 57 populations; 21 665 colonies; 9 326 479 breeding pairs). Colony sizes were highly variable both within and between species. We estimated the proportion of between‐species variation using the repeatability statistic. Colony size‐related statistics of CSFDs (e.g. geometric mean) showed high repeatabilities (R = 0.73–0.88), and shape‐related measures ranged from null (kurtosis), moderate (fit to a log‐normal distribution, R = 0.62) to highly repeatable (e.g. skewness, R = 0.74–0.87). We thus show that species collective patterns can be at the same time highly variable within species and a robust species‐specific trait that bridge ecological spatio‐temporal heterogeneities.     

The effects of colony characteristics on life span and foraging behavior of individual wasps (Polybia occidentalis,Hymenoptera: Vespidae)

Summary We studied the effects of intrinsic colony characteristics and an imposed contingency on the life span and behavior of foragers in the swarm-founding social waspPolybia occidentalis. Data were collected on marked, known-age workers introduced into four observation colonies.To test the hypothesis that colony demographic features affect worker life span, we examined the relationships of colony age and size with worker life span using survivorship analysis. Colony age and size had positive relationships with life span; marked workers from two larger, older colonies had longer life spans (¯X = 24.7 days) than those from two smaller, younger colonies (¯X = 20.1 days).We quantified the effects of experimentally imposed nest damage on forager behavior, to determine which of three predicted behavioral responses by foragers to this contingency (increased probability of foraging for building material, increased rate of foraging, or decrease in age of onset of foraging) would be employed. Increasing the colony level of need for materials used in nest construction (wood pulp and water) by damaging the nests of two colonies did not cause an increase in either the proportion of marked workers that gathered nest materials or in foraging rates of marked individuals, when compared with introduced workers in two simultaneously observed control colonies. Instead, nest damage caused a decrease in the age at which marked workers first foraged for pulp and water. The response to an increase in the need for building materials was an acceleration of behavioral development in some workers.     

Intraspecific variation in size and density of Avocet colonies: effects of nest-distances on hatching and breeding success

In many colonial bird species there is considerable intraspecific variation in colony size and inter‐nest distance (colony density). Possible causes of this variation and its effects on hatching success (survival of eggs) and breeding success (probability of a pair raising chicks) were studied in 48 Avocet Recurvirostra avosetta colonies in Schleswig‐Holstein (Germany) between 1991 and 1996. Colony density was influenced by time of year and habitat (categories: island or mainland, close to or far from feeding grounds). Colonies on islands had the highest densities. When all available space at a colony site was used, colonies became very dense (mean nearest‐neighbour nest distance less than 1 m). Colony size (number of clutches) was influenced by time of year, but not by habitat. Hatching success was low in high density colonies and in very low density ‘colonies’ (single nests) and high over a broad range of intermediate nest densities. The low success rate of single nests was caused by a very high predation rate, whereas the low success rate in very dense colonies was caused by a high rate of nest abandonment. Nest abandonment in very dense colonies was associated with a high level of aggressiveness among Avocets during the egg‐laying period. Due to territorial behaviour, Avocets seemed to be expelled from the densest breeding sites. In very dense colonies, high frequencies of clutches of unusual size occurred due to conspecific nest parasitism. The number of Avocets taking part in attacks on potential egg predators was small and (in colonies of more than one clutch) depended neither on colony size nor on colony density. Despite a low hatching success in very dense colonies, individuals breeding in the densest colonies had significantly better chances of raising chicks than Avocets breeding in less dense colonies. Coloniality seemed to be obligatory for Avocets in order to ensure hatching success. The size and density of colonies seemed to be associated with the availability of suitable nesting habitats (islands).     

Enumeration and isolation of anaerobic microbiota of piggery wastes.

Media for enumeration of the microbiota of anaerobically stored piggery wastes were tested. Highest colony counts were obtained with 80 to 100% farm slurry supernatant included in the anaerobic roll tube media. Colony counts with these media numbered 2 X 10(9) to 12 X 10(9)/g (wet weight), which represents about 20% of the microscopic counts. Lower percentages of slurry supernatant in the media gave lower colony counts. Addition of glucose, cellobiose, and starch or of Trypticase to media with 20% slurry supernatant did not increase colony counts. Higher values were obtained when hemicellulose preparations were added to these media. Incubation at 25 degrees C gave the highest numbers. Incubation at 15 to 37 degrees C gave counts of about 70 and 10%, respectively, of those at 25 degrees C. Of the colonies picked for isolation, about 20% were obtained in pure culture. The isolates apparently belonged to the genera Peptococcus, Ruminococcus, Peptococcus, Ruminococcus, Pepostreptococcus, and Bacteroides.     

Enumeration and isolation of anaerobic microbiota of piggery wastes

Media for enumeration of the microbiota of anaerobically stored piggery wastes were tested. Highest colony counts were obtained with 80 to 100% farm slurry supernatant included in the anaerobic roll tube media. Colony counts with these media numbered 2 X 10(9) to 12 X 10(9)/g (wet weight), which represents about 20% of the microscopic counts. Lower percentages of slurry supernatant in the media gave lower colony counts. Addition of glucose, cellobiose, and starch or of Trypticase to media with 20% slurry supernatant did not increase colony counts. Higher values were obtained when hemicellulose preparations were added to these media. Incubation at 25 degrees C gave the highest numbers. Incubation at 15 to 37 degrees C gave counts of about 70 and 10%, respectively, of those at 25 degrees C. Of the colonies picked for isolation, about 20% were obtained in pure culture. The isolates apparently belonged to the genera Peptococcus, Ruminococcus, Peptococcus, Ruminococcus, Pepostreptococcus, and Bacteroides.     

Automated counting of mammalian cell colonies by means of a flat bed scanner and image processing.

BACKGROUND: Clonogenic assays are used frequently to measure the cell killing and mutagenic effects of radiation and other agents. Clonogenic assays carried out manually are tedious and time-consuming and involve a significant element of subjectivity. However, several commercial automatic colony counters are available. Based on CCD video imaging and image analysis they are relatively expensive and can analyze only one petri dish at a time. METHOD: We have developed a cheaper and more efficient device, which employs a flat bed scanner to image 12 60-mm petri dishes at a time. Two major problems in automated colony counting are the clustering of colonies and edge effects. By using standard image analysis and implementing an inflection point algorithm, these problems were greatly diminished. The resulting system was compared with two manual colony counts, as well as with automated counts with the Oxford Optronix ColCount colony counter for cell lines V79 and HaCaT. RESULTS: Comparisons assuming the manual counts to be correct showed that our automatic counter was slightly more accurate than the commercial unit. CONCLUSIONS: As a whole, our automated colony counter performed significantly better than the commercial unit with regard to processing time, cost and accuracy.