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Title: An Open-Source Workflow for Spatiotemporal Studies with COVID-19 as an Example
Many previous studies have shown that open-source technologies help democratize information and foster collaborations to enable addressing global physical and societal challenges. The outbreak of the novel coronavirus has imposed unprecedented challenges to human society. It affects every aspect of livelihood, including health, environment, transportation, and economy. Open-source technologies provide a new ray of hope to collaboratively tackle the pandemic. The role of open source is not limited to sharing a source code. Rather open-source projects can be adopted as a software development approach to encourage collaboration among researchers. Open collaboration creates a positive impact in society and helps combat the pandemic effectively. Open-source technology integrated with geospatial information allows decision-makers to make strategic and informed decisions. It also assists them in determining the type of intervention needed based on geospatial information. The novelty of this paper is to standardize the open-source workflow for spatiotemporal research. The highlights of the open-source workflow include sharing data, analytical tools, spatiotemporal applications, and results and formalizing open-source software development. The workflow includes (i) developing open-source spatiotemporal applications, (ii) opening and sharing the spatiotemporal resources, and (iii) replicating the research in a plug and play fashion. Open data, open analytical tools and source code, more » and publicly accessible results form the foundation for this workflow. This paper also presents a case study with the open-source spatiotemporal application development for air quality analysis in California, USA. In addition to the application development, we shared the spatiotemporal data, source code, and research findings through the GitHub repository. « less
Authors:
; ; ; ;
Award ID(s):
1841520
Publication Date:
NSF-PAR ID:
10398242
Journal Name:
ISPRS International Journal of Geo-Information
Volume:
11
Issue:
1
Page Range or eLocation-ID:
13
ISSN:
2220-9964
Sponsoring Org:
National Science Foundation
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Over the past two years, we have accumulated significant experience with how to scan a diverse inventory of slides using the Aperio AT2 high-volume scanner. We have been working closely with the vendor to resolve many problems associated with the use of this scanner for research purposes. This scanning project began in January of 2018 when the scanner was first installed. The scanning process was slow at first since there was a learning curve with how the scanner worked and how to obtain samples from the hospital. From its start date until May of 2019 ~20,000 slides we scanned. In the past 6 months from May to November we have tripled that number and how hold ~60,000 slides in our database. This dramatic increase in productivity was due to additional undergraduate staff members and an emphasis on efficient workflow. The Aperio AT2 scans 400 slides a day, requiring at least eight hours of scan time. The efficiency of these scans can vary greatly. When our team first started, approximately 5% of slides failed the scanning process due to focal point errors. We have been able to reduce that to 1% through a variety of means: (1) best practices regarding daily and monthly recalibrations, (2) tweaking the software such as the tissue finder parameter settings, and (3) experience with how to clean and prep slides so they scan properly. Nevertheless, this is not a completely automated process, making it very difficult to reach our production targets. With a staff of three undergraduate workers spending a total of 30 hours per week, we find it difficult to scan more than 2,000 slides per week using a single scanner (400 slides per night x 5 nights per week). The main limitation in achieving this level of production is the lack of a completely automated scanning process, it takes a couple of hours to sort, clean and load slides. 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