Icy: an open bioimage informatics platform for extended reproducible research

2012 ◽  
Vol 9 (7) ◽  
pp. 690-696 ◽  
Author(s):  
Fabrice de Chaumont ◽  
Stéphane Dallongeville ◽  
Nicolas Chenouard ◽  
Nicolas Hervé ◽  
Sorin Pop ◽  
...  
2021 ◽  
Author(s):  
Haoran Chen ◽  
Robert F. Murphy

AbstractCell segmentation is a cornerstone of many bioimage informatics studies. Inaccurate segmentation introduces computational error in downstream cellular analysis. Evaluating the segmentation results is thus a necessary step for developing the segmentation methods as well as choosing the most appropriate one for a certain kind of tissue or image. The evaluation process has typically involved comparison of segmentations to those generated by humans, which can be expensive and subject to unknown bias. We present here an approach that seeks to evaluate cell segmentation methods without relying upon comparison to results from humans. For this, we defined a number of segmentation quality metrics that can be applied to multichannel fluorescence images. We calculated these metrics for 11 previously-described segmentation methods applied to datasets from 5 multiplexed microscope modalities covering 5 tissues. Using principal component analysis to combine the metrics we defined an overall cell segmentation quality score and ranked the segmentation methods. A Reproducible Research Archive containing all data and code will be made available upon publication at http://hubmap.scs.cmu.edu.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shahzad Ahmed ◽  
Dingyang Wang ◽  
Junyoung Park ◽  
Sung Ho Cho

AbstractIn the past few decades, deep learning algorithms have become more prevalent for signal detection and classification. To design machine learning algorithms, however, an adequate dataset is required. Motivated by the existence of several open-source camera-based hand gesture datasets, this descriptor presents UWB-Gestures, the first public dataset of twelve dynamic hand gestures acquired with ultra-wideband (UWB) impulse radars. The dataset contains a total of 9,600 samples gathered from eight different human volunteers. UWB-Gestures eliminates the need to employ UWB radar hardware to train and test the algorithm. Additionally, the dataset can provide a competitive environment for the research community to compare the accuracy of different hand gesture recognition (HGR) algorithms, enabling the provision of reproducible research results in the field of HGR through UWB radars. Three radars were placed at three different locations to acquire the data, and the respective data were saved independently for flexibility.


Author(s):  
Andreas Weiler ◽  
Harry Schilling ◽  
Lukas Kircher ◽  
Michael Grossniklaus

Geophysics ◽  
2017 ◽  
Vol 82 (6) ◽  
pp. WBi-WBii ◽  
Author(s):  
Filippo Broggini ◽  
Joseph Dellinger ◽  
Sergey Fomel ◽  
Yang Liu

Author(s):  
Andy Hector

Statistics is a fundamental component of the scientific toolbox, but learning the basics of this area of mathematics is one of the most challenging parts of a research training. This book gives an up-to-date introduction to the classical techniques and modern extensions of linear-model analysis—one of the most useful approaches in the analysis of scientific data in the life and environmental sciences. The book emphasizes an estimation-based approach that takes account of recent criticisms of overuse of probability values and introduces the alternative approach using information criteria. The book is based on the use of the open-source R programming language for statistics and graphics, which is rapidly becoming the lingua franca in many areas of science. This second edition adds new chapters, including one discussing some of the complexities of linear-model analysis and another introducing reproducible research documents using the R Markdown package. Statistics is introduced through worked analyses performed in R using interesting data sets from ecology, evolutionary biology, and environmental science. The data sets and R scripts are available as supporting material.


2021 ◽  
Vol 13 (2) ◽  
pp. 100-108
Author(s):  
K.V. Vorontsov ◽  
V.I. Iglovikov ◽  
V.V. Strijov ◽  
A.E. Ustuzhanin ◽  
A.S. Khritankov

Author(s):  
Jessica M Hoffman ◽  
Caesar M Hernandez ◽  
Abbi R Hernandez ◽  
Jennifer L Bizon ◽  
Sara N Burke ◽  
...  

Abstract While neurodegenerative diseases can strike at any age, the majority of afflicted individuals are diagnosed at older ages. Due to the important impact of age in disease diagnosis, the field of neuroscience could greatly benefit from the many of the theories and ideas from the biology of aging – now commonly referred as geroscience. As discussed in our complementary perspective on the topic, there is often a “silo-ing” between geroscientists who work on understanding the mechanisms underlying aging and neuroscientists who are studying neurodegenerative diseases. While there have been some strong collaborations between the biology of aging and neuroscientists, there is still great potential for enhanced collaborative effort between the two fields. To this end, here, we review the state of the geroscience field, discuss how neuroscience could benefit from thinking from a geroscience perspective, and close with a brief discussion on some of the “missing links” between geroscience and neuroscience and how to remedy them. Notably, we have a corresponding, concurrent review from the neuroscience perspective. Our overall goal is to “bridge the gap” between geroscience and neuroscience such that more efficient, reproducible research with translational potential can be conducted.


CSA News ◽  
2015 ◽  
Vol 60 (10) ◽  
pp. 22-22
Author(s):  
Michael Young ◽  
Todd Skaggs

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