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scikit-image: image processing in Python

Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
2014 PeerJ  
scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications.  ...  In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image.  ...  We also acknowledge the efforts of the more than 100 contributors to the scikit-image code base:  ... 
doi:10.7717/peerj.453 pmid:25024921 pmcid:PMC4081273 fatcat:mrtt3tdogbeplikl7gnc6yv6zm


L. Annala, M. A. Eskelinen, J. Hämäläinen, A. Riihinen, I. Pölönen
2018 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences  
They also fulfill our goal of easy and agile data processing. In this paper we will present our processing pipeline and demonstrate it in practice.  ...  Python is a very popular programming language among data scientists around the world. Python can also be used in hyperspectral data analysis.  ...  Scikit-image is a sister package of scikit-learn. Scikit-image is focused on computer vision and image processing. The same advantages as with scikit-learn apply here.  ... 
doi:10.5194/isprs-archives-xlii-3-45-2018 fatcat:2hvohnnpsfcfbawvydgpzm3die

Analyzing microtomography data with Python and the scikit-image library

Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
2016 Advanced Structural and Chemical Imaging  
Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats  ...  from a rich scientific Python ecosystem that contains many powerful libraries for tasks such as visualization or machine learning. scikit-image combines a gentle learning curve, versatile image processing  ...  CREMI ( is acknowledged for the membrane image of Fig. 5b.  ... 
doi:10.1186/s40679-016-0031-0 pmid:29142808 pmcid:PMC5660892 fatcat:2enedrit3berlgg4nmbqnlqcjy

pyparty: Blob Detection, Drawing and Manipulation in Python

Adam Hughes
2014 Journal of Open Research Software  
In the last few years, image processing and computer vision in Python has rapidly matured 1 with the emergence of libraries like scikit-image [3] , Mahotas [4] , and SimpleCV [5] . scikit-image and  ...  Notes 1 SciPy's ndimage collection pre-dates scikit-image for example. 2 Cell profiler [12] is a great example of a specialized microscopy application in Python.  ... 
doi:10.5334/ fatcat:kctgjubdmjedlk4nskp3e4ag5m

Python - Based Image Processing

Mrs. Asha K H, Manjunathswamy B E, Mrs. Chaithra A S
2021 International Journal of Scientific Research and Management  
In other terms, image processing is the process of neutering and analysing graphical information in photographs. In our lives, we frequently come across many types of image processing.  ...  The main goal of image processing is to transform photos in the desired way.  ...  In recent years, Python has grown in popularity in the field of digital image processing.  ... 
doi:10.18535/ijsrm/v9i11.ec03 fatcat:zlo6y3vjvjddrgigwzcvq5vldu


T.R. Ravi, Kshitij Kuhikar, Yashaswi Kalambe, Ameya Wagh, Utkarsha Deshkar
2020 Journal of research in engineering and applied sciences  
and image recognition library that implements the basic image manipulation and processing using the core scientific modules NumPy and SciPy.  ...  This paper aims to present an overview of a project developed to introduce an element of automation to this hectic procedure and explores the open source library Scikitimage which is an image processing  ...  Acknowledgement The authors would like to thank government body NBSS & LUP located in Nagpur to share their problem definition with us of automating detection of wells and to give us opportunity to work  ... 
doi:10.46565/jreas.2020.v05i04.004 fatcat:raqt4cdanvhcdmddwuxvr6qpiu

A Review of Watershed Implementations for Segmentation of Volumetric Images

Anton Kornilov, Ilia Safonov, Ivan Yakimchuk
2022 Journal of Imaging  
In addition, we forecast future directions of software development for 3D image segmentation by watershed.  ...  In particular, the difference among various implementations is noticeable for huge volumetric images; for instance, tomographic 3D images, for which low performance and high memory requirements of watershed  ...  SMIL and ITK process a given FIB-SEM image in about 10 min. Watershed execution time of an Scikit-image with WL construction is absolutely unacceptable.  ... 
doi:10.3390/jimaging8050127 pmid:35621890 fatcat:h2h2yv2tv5calmkyn25rxdiaiq

A Solid Foundation for Statistics in Python with SciPy

Warren Weckesser, Matt Haberland
2020 Zenodo  
scikit-image, scikit-learn, Biopython, PsychoPy, ... • The web page has over 3000 journal citations.  ...  SciPy -The Library • Core library in the Python scientific computing ecosystem. • Started in 2001, currently downloaded millions of times each year. • Over 6000 other packages depend on SciPy, including  ...  A Solid Foundation for Statistics in Python with SciPy What do you hope to achieve by learning from or collaborating with other grantees?  ... 
doi:10.5281/zenodo.3840596 fatcat:ciibbp3xzvdsvb4al23sr63bhu

IPART: A Python Package for Image-Processing based Atmospheric River Tracking

Guangzhi Xu, Xiaohui Ma, Ping Chang
2020 Journal of Open Source Software  
The detection process utilizes the image-processing package scikit-image (Walt et al., 2014) . The AR axis finding process utilizes the networkx package (Hagberg et al., 2008) .  ...  The algorithms are implemented using the Python programming language as a wrapper to some well-established numeric packages including numpy, scikit-image and networkx etc.  ... 
doi:10.21105/joss.02407 fatcat:gnlivn7x5jd6fjxru7wnlqwkcm

Investigating Type Declaration Mismatches in Python

Luca Pascarella, Achyudh Ram, Azqa Nadeem, Dinesh Bisesser, Norman Knyazev, Alberto Bacchelli
2018 Zenodo  
In dynamically typed languages, such as Python, an inconsistency in the documentation may lead to a mismatch in type declarations only visible at runtime.  ...  With our study, we investigate how often the documentation is inconsistent in a sample of 239 methods from five Python open- source software projects.  ...  With this process, we selected five heterogeneous software systems: SCIKIT-LEARN, SCIKIT-IMAGE, MATPLOTLIB, NETWORKX, and NEUPY.  ... 
doi:10.5281/zenodo.1690677 fatcat:zpelvbxjfngylofwly7qciwmxe

jicbioimage: a tool for automated and reproducible bioimage analysis

Tjelvar S. G. Olsson, Matthew Hartley
2016 PeerJ  
There has been steady improvement in methods for capturing bioimages. However analysing these images still remains a challenge.  ...  It has a wide range of supporting libraries for image processing but lacks native support for common bioimage formats, and requires specific code to be written to ensure that suitable audit trails are  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.2674 pmid:27896026 pmcid:PMC5119319 fatcat:7vidgadyinee3pomshq4jc6m7a

Rapid development of image analysis research tools: Bridging the gap between researcher and clinician with pyOsiriX

Matthew D. Blackledge, David J. Collins, Dow-Mu Koh, Martin O. Leach
2016 Computers in Biology and Medicine  
Using pyOsiriX we hope to bridge the apparent gap between basic imaging scientists and clinical practice in a research setting and thus accelerate the development of advanced clinical image processing.  ...  We have demonstrated that good segmentation can be achieved for two example CT studies by using a combination of Python libraries including scikit-learn, scikit-image, SimpleITK and matplotlib.  ...  using NumPy [46] , scientific computing using SciPy [50] , extensive plotting routines with matplotlib [48] , advanced image processing with scikit-image [50] , state-of-the-art machine learning using  ... 
doi:10.1016/j.compbiomed.2015.12.002 pmid:26773941 pmcid:PMC4761020 fatcat:rslit7k3andj5ps2g3yjh3hksy

Pooch: A friend to fetch your data files

Leonardo Uieda, Santiago Soler, Rémi Rampin, Hugo van Kemenade, Matthew Turk, Daniel Shapero, Anderson Banihirwe, John Leeman
2020 Journal of Open Source Software  
A common approach is to include smaller datasets in the GitHub repository directly and package them with the source and binary distributions (e.g., scikit-learn (Pedregosa et al., 2011) and scikit-image  ...  Pooch is written in pure Python and has minimal dependencies.  ... 
doi:10.21105/joss.01943 fatcat:4z272rpvljambm5wcqm5f646he

Investigating type declaration mismatches in Python

Luca Pascarella, Achyudh Ram, Azqa Nadeem, Dinesh Bisesser, Norman Knyazev, Alberto Bacchelli
2018 2018 IEEE Workshop on Machine Learning Techniques for Software Quality Evaluation (MaLTeSQuE)  
In dynamically typed languages, such as Python, an inconsistency in the documentation may lead to a mismatch in type declarations only visible at runtime.  ...  In dynamically typed languages, such as Python, an inconsistency in the documentation may lead to a mismatch in type declarations only visible at runtime.  ...  With this process, we selected five heterogeneous software systems: SCIKIT-LEARN, SCIKIT-IMAGE, MATPLOTLIB, NETWORKX, and NEUPY.  ... 
doi:10.1109/maltesque.2018.8368458 dblp:conf/wcre/PascarellaRNBKB18 fatcat:llykgmqzazaxxcyep5rdp7g6i4

Data Processing Using Python in DigitalMicrograph

Benjamin Miller, Stephen Mick
2020 Microscopy and Microanalysis  
An example of this is shown in Figure 1 , where dendrite growth during a single second is measured from 75 frames using an image segmentation technique implemented with functions from scikit-image.  ...  Since Python is a widely adopted scripting language [4], its integration into GMS makes TEM data processing accessible to far more researchers.  ... 
doi:10.1017/s1431927620017213 fatcat:n6hauxak45bszjhwi6liiqg5sm
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