scholarly journals The Charcoal Quantification Tool (CharTool): A Suite of Open-source Tools for Quantifying Charcoal Fragments and Sediment Properties in Archaeological and Paleoecological Analysis

2020 ◽  
Vol 11 (1) ◽  
pp. 103-115
Author(s):  
Grant Snitker
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Digital Image Analysis ◽  
Multiple Scales ◽  
Low Cost ◽  
Open Science ◽  
Charcoal Analysis ◽  
Sediment Properties ◽  
Standard Methods ◽  
Free Open Source

Sedimentary charcoal analysis is increasingly used in archaeological and paleoecological research to examine human-environmental relationships at multiple scales. The recent availability of low-cost digital microscopes and imaging software has resulted in the rapid adoption of digital image analysis in charcoal studies. However, most published studies include only minimal accounts of software configurations or utilize proprietary image analysis programs, thus hindering replication, standardization, and comparability of charcoal analyses across the field. In an effort to encourage replicable methods and a culture of open science, this paper presents the Charcoal Quantification Tool (CharTool), a free, open-source suite of charcoal and sediment quantification tools designed for use with ImageJ. CharTool blends standard methods in visual and digital charcoal analysis to increase the analyst’s participation in identifying and measuring charcoal metrics. Each CharTool module is described and demonstrated in a vignette using sedimentary charcoal collected from the Son Servera study area, Mallorca, Spain. A suggested workflow, user-guide, scripted analyses for processing outputs, and download instructions are included as supplementary materials to this article.

scholarly journals Droplet image analysis with user-friendly freeware CellProfiler

2020 ◽  
Vol 12 (17) ◽  
pp. 2287-2294
Author(s):  
Simona Bartkova ◽  
Marko Vendelin ◽  
Immanuel Sanka ◽  
Pille Pata ◽  
Ott Scheler
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
User Friendly ◽  
Free Open Source

We show how to use free open-source CellProfiler for droplet microfluidic image analysis.

scholarly journals Open Science Framework (OSF)

2017 ◽  
Vol 105 (2) ◽  
Author(s):  
Erin D. Foster, MSLS ◽  
Ariel Deardorff, MLIS
Keyword(s):  
Open Source ◽  
Web Application ◽  
Open Science ◽  
Science Framework ◽  
Free Open Source

The Open Science Framework (OSF) is a free, open source, research workflow web application developed and maintained by the Center for Open Science (COS).

Quantitative Analysis of Historic Mortars by Digital Image Analysis of Thin Sections

2019 ◽  
Vol 23 (2) ◽  
pp. 83-92 ◽  
Author(s):  
Bernhard Middendorf ◽  
Tim Schade ◽  
Karin Kraus
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Thin Section ◽  
Digital Image ◽  
Digital Image Analysis ◽  
Traditional Methods ◽  
Thin Sections ◽  
Open Source Program ◽  
Source Program ◽  
Historic Mortar

Abstract In restoration work, the compatibility between old and new building material is the key point for sustainable repair of buildings or monuments. Consequently, conservation scientists are looking for an alternative method to the traditional procedures to determine the aggregate grading curve and the binder/aggregate-ratio of the historic material. The problem of using the traditional methods is the frequent major intervention in an existing building. These destructive methods are not allowed. Whereas, to get information about the historic mortar, a new technique, the digital image analysis (DIA), is applied in this paper. Moreover, small amounts of the historic material have already been prepared as thin sections and analysed with a microscope. Modern microscopy techniques allow investigations of quantitative and qualitative composition of historic material. Incentive of this work was to get all the required information to recreate the historic mortar by using the DIA with an open source program only at one thin section. In addition, to examine the accuracy and the significance of the DIA, all results were compared with a known mixture, and in a second test series, the results of the DIA were compared with the traditional methods. The results show that the DIA of thin sections of a historic mortar is highly effective for analysing decisive factors like the binder/aggregate-ratio and the grading curve of the aggregates. Furthermore, it is possible to analyse the mortar only by having one thin section using an open source program ImageJ. Especially in the case of carbonate rock as aggregate, DIA is the only method to analyse these characteristics of a mortar.

3D Virtual Planning for Rhinoplasty Using a Free Add-On for Open-Source Software

2021 ◽  
Author(s):  
Davi S Sobral ◽  
Daniele W Duarte ◽  
Rodrigo F V Dornelles ◽  
Cícero A C Moraes
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Healthcare Providers ◽  
Three Dimensional ◽  
Positive Outcomes ◽  
Virtual Planning ◽  
Good Communication ◽  
Design Software ◽  
Free Open Source

Abstract Background Rhinoplasty is one of the most frequent aesthetic surgeries; the procedure can be challenging for inexperienced surgeons, and positive outcomes depend on good communication with the patient, proper planning, and precise execution. Three-dimensional (3D) technology has emerged to address these issues, but specific software for 3D planning tends to be expensive. Objectives This study presents a simple, low-cost method for 3D simulation to plan rhinoplasty. Methods This preliminary report describes 3D rhinoplasty planning in a series of 3 cases employing free software and an add-on especially developed for rhinoplasty (Blender and RhinOnBlender, respectively). The photogrammetry protocol, which can be performed easily with a smartphone, is described in detail along with all the steps in 3D planning. Results The software and add-on automated the process, making the tool environment accessible to surgeons who are not familiar with graphic design software. The surgeries were uneventful in all cases, and the patients were satisfied with the outcomes. Conclusions 3D graphic technology has provided significant advances in health research, improvement, and teaching for surgeons and communication between surgeons and patients. Free open-source software and add-ons are excellent options that offer proven utility, affordability, and ease of utilization to healthcare providers.

scholarly journals Digital Image Analysis of the Angle and Optic Nerve: A Simple, Fast, and Low-Cost Method for Glaucoma Assessment

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Greg Russell ◽  
Silvia N. W. Hertzberg ◽  
Natalia Anisimova ◽  
Natalia Gavrilova ◽  
Beáta É. Petrovski ◽  
...  
Keyword(s):  
Image Analysis ◽  
Optic Nerve ◽  
Nerve Fiber ◽  
Digital Image ◽  
Digital Image Analysis ◽  
Low Cost ◽  
Detection Methods ◽  
Slit Lamp ◽  
Image Subtraction ◽  
Oct Imaging

Purpose. To devise a simple, fast, and low-cost method for glaucoma assessment using digital image analysis of the angle and optic nerve in human subjects. Methods. Images from glaucoma and fundus assessment were used in this study, including color fundus photographs, standard optic nerve optical coherence tomography (OCT), and digital slit-lamp images of the angle/gonioscopy. Digital image conversion and analysis of the angle using ImageJ (NIH, USA) and adaptive histogram equalization contrast-limited AHE (CLAHE) to prevent noise amplification were implemented. Angle and optic nerve images were analyzed separately in the red, green, and blue (RGB) channels followed by 3D volumetric analysis of the degrees of angle depth and cup volume of the optic nerve. Horizontal tomogram reconstitution and nerve fiber detection methods were developed and compared to standard OCT images. Results. Digital slit-lamp angle images showed similar accuracy as standard anterior OCT measurements. Comparative analysis of RGB channels produced volumetric cup and horizontal tomogram, which closely resembled the 3D OCT appearance and B-scan of the cup, respectively. RGB channel splitting and image subtraction produced a map closely resembling that of the retinal nerve fiber layer (RNFL) thickness map on OCT. Conclusions. While OCT imaging is rapidly progressing in the area of optic disc and chamber angle assessment, rising healthcare costs and lack of availability of the technology open a demand for alternative and cost-minimizing forms of image analysis in glaucoma. Volumetric, geometric, and segmentational data obtained through digital image analysis correspond well to those obtained by OCT imaging.

scholarly journals Application of Digital Image Analysis to the Prediction of Chlorophyll Content in Astragalus Seeds

2021 ◽  
Vol 11 (18) ◽  
pp. 8744
Author(s):  
Yanan Xu ◽  
Keling Tu ◽  
Ying Cheng ◽  
Haonan Hou ◽  
Hailu Cao ◽  
...  
Keyword(s):  
Image Analysis ◽  
Chlorophyll Content ◽  
Digital Image ◽  
Digital Image Analysis ◽  
Low Cost ◽  
High Price ◽  
Multiple Features ◽  
Characteristic Features ◽  
Mlp Model

Chlorophyll fluorescence (CF) has been applied to measure the chlorophyll content of seeds, in order to determine seed maturity, but the high price of equipment limits its wider application. Astragalus seeds were used to explore the applicability of digital image analysis technology to the prediction of seed chlorophyll content and to supply a low cost and alternative method. Our research comprised scanning and extracting the characteristic features of Astragalus seeds, determining the chlorophyll content, and establishing a predictive model of chlorophyll content in Astragalus seeds based on characteristic features. The results showed that the R2 of the MLR prediction model established with multiple features was ≥0.947, and the R2 of the MLP model was ≥0.943. By sorting of two single features, the R and G values, the R2 reached 0.969 and 0.965, respectively. A germination result showed that the lower the chlorophyll content, the higher the quality of the seeds. Therefore, we draw a conclusion that digital image analysis technology can be used to predict effectively the chlorophyll content of Astragalus seeds, and provide a reference for the selection of mature and viable Astragalus seeds.

scholarly journals DIGITAL IMAGE ANALYSIS BASED ON AUTOMATED COUNTING CLUSTERED SOYBEAN SEEDS

2014 ◽  
Vol 12 (3) ◽  
pp. 3325-3328
Author(s):  
Jasdeep Kaur
Keyword(s):  
Image Analysis ◽  
Digital Image ◽  
Digital Image Analysis ◽  
Low Cost ◽  
Detection Algorithm ◽  
Soya Bean ◽  
Soybean Seeds ◽  
Manual Counting ◽  
Processing Steps ◽  
Image Analysis Techniques

-  This paper investigates the use of digital image analysis techniques for developing for counting clustered soya bean seeds. Images are extracted from source WWW.21food.com). As manual counting have several issues such as low accuracy and higher cost. Automated counting techniques give a fast and low cost of counting soya bean seeds. This paper follows 5 processing steps. First process converting the image into gray scale and thresholding is applied using CLAHE. Second dilation is applied to enhance the image. Third applied masking to enhance the image. Fourth edge detection algorithm is applied. Fifth step beans extracted with respect to bean shape. 

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