Republication – APD Colony Counter App: Using Watershed Algorithm for improved colony counting

AbstractBased on the current knowledge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission, wearing a mask has been recommended during the COVID-19 pandemic. Bacterial filtration efficiency (BFE) measurements enable designing and regulating medical masks to prevent bioaerosol dissemination; however, despite the simplicity of these measurements, several scientific questions remain unanswered regarding BFE tests. Here, we investigated (1) the impact of substituting 100-mm Petri dishes with 90-mm disposable Petri dishes, (2) the impact of colony-counting methods on the bioaerosol aerodynamic size, and (3) the impact of colony-counting methods on the total viable particle counts. We demonstrated that disposable 90-mm Petri dishes can be used to replace the 100-mm dishes. We also showed that an automatic high-resolution colony counter can be used to directly count viable particles on collection substrates and to measure the bioaerosol size parameters. Our results enable possible modernization of the outdated testing methods recommended in the US and European standards for BFE measurements. Specifically, use of a modernized colony counter should be clearly regulated and permitted to avoid the counting of positive holes. The median aerodynamic diameter appears to be the most relevant parameter for characterizing bioaerosol size.

Download Full-text

Colonizer: Anandroid OS based automated microbial colony counter

10.7287/peerj.preprints.2792 ◽

2017 ◽

Author(s):

Shashwat Kumar ◽

Rudra Vaswata Roy Choudhury ◽

Sunil Laxman

Keyword(s):

Image Analysis ◽

Colony Forming Units ◽

Colony Counting ◽

Wide Range ◽

Colony Counter

Colony counting to estimate colony forming units (CFUs) is a standard microbiology procedure used for determining the number of viable microbes in a system. Typically this process is done manually, which is time consuming, tedious, and sometimes error prone. Alternate image analysis based systems are also time consuming. In this paper we develop and demonstrate a simpleandroid based automated colony counter, called Colonizer, also made freely available on Google Playstore. Our algorithm can also threshold and segment overlapping colonies and thus provide rapid, accurate counts across a wide range of colony densities (from 50-500 colonies/plate), for different microbes, using any android based phone or device.

Download Full-text

Automated Bacterial Colony Counting for Clonogenic Assay

Dental Computing and Applications ◽

10.4018/978-1-60566-292-3.ch009 ◽

2011 ◽

pp. 134-145

Author(s):

Wei-Bang Chen ◽

Chengcui Zhang

Keyword(s):

Digital Images ◽

Clonogenic Assay ◽

Cost Effective ◽

Point Of View ◽

Bacterial Colony ◽

Essential Tool ◽

Colony Counting ◽

Fully Automatic ◽

Colony Counter

Bacterial colony enumeration is an essential tool for many widely used biomedical assays. This chapter introduces a cost-effective and fully automatic bacterial colony counter which accepts digital images as its input. The proposed counter can handle variously shaped dishes/plates, recognize chromatic and achromatic images, and process both color and clear medium. In particular, the counter can detect dish/plate regions, identify colonies, separate aggregated colonies, and finally report consistent and accurate counting result. The authors hope that understanding the complicated and labor-intensive nature of colony counting will assist researchers in a better understanding of the problems posed and the need to automate this process from a software point of view, without relying too much on specific hardware.

Download Full-text

Colonizer: Anandroid OS based automated microbial colony counter

10.7287/peerj.preprints.2792v1 ◽

2017 ◽

Author(s):

Shashwat Kumar ◽

Rudra Vaswata Roy Choudhury ◽

Sunil Laxman

Keyword(s):

Image Analysis ◽

Colony Forming Units ◽

Colony Counting ◽

Wide Range ◽

Colony Counter

Colony counting to estimate colony forming units (CFUs) is a standard microbiology procedure used for determining the number of viable microbes in a system. Typically this process is done manually, which is time consuming, tedious, and sometimes error prone. Alternate image analysis based systems are also time consuming. In this paper we develop and demonstrate a simpleandroid based automated colony counter, called Colonizer, also made freely available on Google Playstore. Our algorithm can also threshold and segment overlapping colonies and thus provide rapid, accurate counts across a wide range of colony densities (from 50-500 colonies/plate), for different microbes, using any android based phone or device.

Download Full-text

EFEKTIVITAS ANTIBAKTERI BAWANG PUTIH (Allium sativum L) SEBAGAI PENGAWET ALAMI PADA IKAN LELE DUMBO (Clarias gariephinus) SEGAR

Surya Medika: Jurnal Ilmiah Ilmu Keperawatan dan Ilmu Kesehatan Masyarakat ◽

10.32504/sm.v14i1.106 ◽

2019 ◽

Vol 14 (1) ◽

pp. 26

Author(s):

Dyah Anggraeni ◽

Nurlela Nurlela

Keyword(s):

Room Temperature ◽

Allium Sativum ◽

Research Result ◽

Clarias Gariepinus ◽

Storage Period ◽

The Body ◽

Garlic Extract ◽

African Catfish ◽

Natural Preservatives ◽

Colony Counter

Background: Natural preservatives are compounds produced by natural ingredients that can suppress bacterial growth and development. Natural preservatives are carried out because most of the preservatives circulating are chemicals and unsafe for the body. One of the natural preservatives is by using garlic extract (Allium sativum L). Objective: This study is aimed to determine the effectiveness of the antibacterial garlic (Allium sativum L) as a natural preservative in fresh African catfish (Clarias gariepinus). Method: This research used the Pour Plate iroculation method. African catfish (Clarias gariepinus) which is soaked with garlic (Allium sativum L) with a concentration of 7%, 14% and 21% for 30 minutes, then the fish will be kept at room temperature with a storage period of 24 hours and 48 hours and calculated growth in bacterial numbers with the Colony counter. Result: Based on the research result, it was found that garlic extract (Allium sativum L) can obstruct the effectiveness of antibacterial in African catfish (Clarias gariepinus) at a concentration of 14%.

Download Full-text

Segmentation In Medical Resonance images to extract the cancerous nodule for early diagnosis on cancer

INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY ◽

10.24297/ijct.v3i2a.2816 ◽

2012 ◽

Vol 3 (2) ◽

pp. 253-255

Author(s):

Raman Brar

Keyword(s):

Human Lung ◽

Research Work ◽

Vital Role ◽

Watershed Algorithm ◽

Segmentation Method ◽

Resonance Imaging ◽

Segmentation Methods ◽

Segmentation Accuracy ◽

Background Segmentation ◽

Lung Mri

Image segmentation plays a vital role in several medical imaging programs by assisting the delineation of physiological structures along with other parts. The objective of this research work is to segmentize human lung MRI (Medical resonance Imaging) images for early detection of cancer.Watershed Transform Technique is implemented as the Segmentation method in this work. Some comparative experiments using both directly applied watershed algorithm and after marking foreground and computed background segmentation methods show the improved lung segmentation accuracy in some image cases.

Download Full-text

A Novel Vegetation Point Cloud Density Tree-Segmentation Model for Overlapping Crowns Using UAV LiDAR

Remote Sensing ◽

10.3390/rs13081442 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1442

Author(s):

Kaisen Ma ◽

Yujiu Xiong ◽

Fugen Jiang ◽

Song Chen ◽

Hua Sun

Keyword(s):

Point Cloud ◽

Local Maximum ◽

Window Size ◽

Point Clouds ◽

High Density ◽

Watershed Algorithm ◽

Canopy Area ◽

Individual Trees ◽

Optimal Window ◽

Cloud Density

Detecting and segmenting individual trees in forest ecosystems with high-density and overlapping crowns often results in bias due to the limitations of the commonly used canopy height model (CHM). To address such limitations, this paper proposes a new method to segment individual trees and extract tree structural parameters. The method involves the following key steps: (1) unmanned aerial vehicle (UAV)-scanned, high-density laser point clouds were classified, and a vegetation point cloud density model (VPCDM) was established by analyzing the spatial density distribution of the classified vegetation point cloud in the plane projection; and (2) a local maximum algorithm with an optimal window size was used to detect tree seed points and to extract tree heights, and an improved watershed algorithm was used to extract the tree crowns. The proposed method was tested at three sites with different canopy coverage rates in a pine-dominated forest in northern China. The results showed that (1) the kappa coefficient between the proposed VPCDM and the commonly used CHM was 0.79, indicating that performance of the VPCDM is comparable to that of the CHM; (2) the local maximum algorithm with the optimal window size could be used to segment individual trees and obtain optimal single-tree segmentation accuracy and detection rate results; and (3) compared with the original watershed algorithm, the improved watershed algorithm significantly increased the accuracy of canopy area extraction. In conclusion, the proposed VPCDM may provide an innovative data segmentation model for light detection and ranging (LiDAR)-based high-density point clouds and enhance the accuracy of parameter extraction.

Download Full-text

Curcumin-loaded polyvinyl butyral film with antibacterial activity

e-Polymers ◽

10.1515/epoly-2020-0042 ◽

2020 ◽

Vol 20 (1) ◽

pp. 673-681

Author(s):

Yanchao Qiao ◽

Lijie Duan

Keyword(s):

Mechanical Property ◽

Thermal Stability ◽

Antibacterial Activity ◽

Polyvinyl Butyral ◽

Counting Method ◽

E Coli ◽

Antibacterial Materials ◽

Good Antibacterial Activity ◽

Colony Counting ◽

Widespread Interest

AbstractAntibacterial materials have found widespread interest in different fields nowadays. In this study, curcumin (Cur) was incorporated into the polyvinyl butyral (PVB) matrix by dissolving in ethanol for improving the functional properties of a pure PVB film. We found that Cur was uniformly dispersed in the PVB matrix, which showed good compatibility. Moreover, the incorporation of Cur could also improve thermal stability, hydrophilicity, and mechanical property. The UV-vis spectra of the PVB–Cur film demonstrated that the film could block ultraviolet radiation. Subsequently, the antibacterial activity of the PVB–Cur film was measured by the colony-counting method against S. aureus and E. coli. The results showed that the PVB–Cur film exhibited good antibacterial activity. Therefore, the PVB–Cur film was considered as a promising material for food and medical packaging applications.

Download Full-text

Method of famous tea sprout identification and segmentation based on improved watershed algorithm

Computers and Electronics in Agriculture ◽

10.1016/j.compag.2021.106108 ◽

2021 ◽

Vol 184 ◽

pp. 106108

Author(s):

Lei Zhang ◽

Lang Zou ◽

Chuanyu Wu ◽

Jiangming Jia ◽

Jianneng Chen

Keyword(s):

Watershed Algorithm

Download Full-text

mSphere of Influence: the Rise of Artificial Intelligence in Infection Biology

mSphere ◽

10.1128/msphere.00315-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 2

Author(s):

Artur Yakimovich

Keyword(s):

Artificial Intelligence ◽

Machine Learning ◽

Machine Learning Algorithms ◽

Label Free ◽

Edge Label ◽

Bacterial Colony ◽

Link Type ◽

Colony Counting ◽

Anthrax Spores ◽

Infection Biology

ABSTRACT Artur Yakimovich works in the field of computational virology and applies machine learning algorithms to study host-pathogen interactions. In this mSphere of Influence article, he reflects on two papers “Holographic Deep Learning for Rapid Optical Screening of Anthrax Spores” by Jo et al. (Y. Jo, S. Park, J. Jung, J. Yoon, et al., Sci Adv 3:e1700606, 2017, https://doi.org/10.1126/sciadv.1700606) and “Bacterial Colony Counting with Convolutional Neural Networks in Digital Microbiology Imaging” by Ferrari and colleagues (A. Ferrari, S. Lombardi, and A. Signoroni, Pattern Recognition 61:629–640, 2017, https://doi.org/10.1016/j.patcog.2016.07.016). Here he discusses how these papers made an impact on him by showcasing that artificial intelligence algorithms can be equally applicable to both classical infection biology techniques and cutting-edge label-free imaging of pathogens.

Download Full-text