Open Source Tools for Biological Image Analysis

2019 ◽  
pp. 23-37 ◽  
Author(s):  
Romain Guiet ◽  
Olivier Burri ◽  
Arne Seitz
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Biological Image

scholarly journals Wndchrm – an open source utility for biological image analysis

2008 ◽  
Vol 3 (1) ◽  
Author(s):  
Lior Shamir ◽  
Nikita Orlov ◽  
D Mark Eckley ◽  
Tomasz Macura ◽  
Josiah Johnston ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Biological Image

scholarly journals Fiji: an open-source platform for biological-image analysis

2012 ◽  
Vol 9 (7) ◽  
pp. 676-682 ◽  
Author(s):  
Johannes Schindelin ◽  
Ignacio Arganda-Carreras ◽  
Erwin Frise ◽  
Verena Kaynig ◽  
Mark Longair ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Biological Image

A Review of Biological Image Analysis

2018 ◽  
Vol 13 (4) ◽  
pp. 337-343 ◽  
Author(s):  
Weiyang Chen ◽  
Weiwei Li ◽  
Xiangjun Dong ◽  
Jialun Pei
Keyword(s):  
Image Analysis ◽  
Biological Image

The State of the Art in Biological Image Analysis

Cell Biology ◽  
2006 ◽  
pp. 201-206
Author(s):  
F FEDERICI ◽  
S SCAGLIONE ◽  
A DIASPRO
Keyword(s):  
Image Analysis ◽  
State Of The Art ◽  
The State ◽  
Biological Image

scholarly journals Geographic Object-Based Image Analysis for Automated Landslide Detection Using Open Source GIS Software

2019 ◽  
Vol 8 (12) ◽  
pp. 551 ◽  
Author(s):  
Raphael Knevels ◽  
Helene Petschko ◽  
Philip Leopold ◽  
Alexander Brenning
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Land Surface ◽  
Region Growing ◽  
Support Vector ◽  
Visual Interpretation ◽  
Object Based Image Analysis ◽  
Object Based ◽  
Geographic Object ◽  
Gis Software

With the increased availability of high-resolution digital terrain models (HRDTM) generated using airborne light detection and ranging (LiDAR), new opportunities for improved mapping of geohazards such as landslides arise. While the visual interpretation of LiDAR, HRDTM hillshades is a widely used approach, the automatic detection of landslides is promising to significantly speed up the compilation of inventories. Previous studies on automatic landslide detection often used a combination of optical imagery and geomorphometric data, and were implemented in commercial software. The objective of this study was to investigate the potential of open source software for automated landslide detection solely based on HRDTM-derived data in a study area in Burgenland, Austria. We implemented a geographic object-based image analysis (GEOBIA) consisting of (1) the calculation of land-surface variables, textural features and shape metrics, (2) the automated optimization of segmentation scale parameters, (3) region-growing segmentation of the landscape, (4) the supervised classification of landslide parts (scarp and body) using support vector machines (SVM), and (5) an assessment of the overall classification performance using a landslide inventory. We used the free and open source data-analysis environment R and its coupled geographic information system (GIS) software for the analysis; our code is included in the Supplementary Materials. The developed approach achieved a good performance (κ = 0.42) in the identification of landslides.

scholarly journals dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM

2017 ◽  
Vol 77 (21) ◽  
pp. e87-e90 ◽  
Author(s):  
Christian Herz ◽  
Jean-Christophe Fillion-Robin ◽  
Michael Onken ◽  
Jörg Riesmeier ◽  
Andras Lasso ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Quantitative Image Analysis ◽  
Quantitative Image

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 Quantitative analysis of subcellular distributions with an open-source, object-based tool

Biology Open ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. bio055228 ◽  
Author(s):  
Pearl V. Ryder ◽  
Dorothy A. Lerit
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Three Dimensional ◽  
Analysis Data ◽  
Form And Function ◽  
Object Based Image Analysis ◽  
Object Based ◽  
And Function ◽  
Microscopy Images ◽  
Complete Process

ABSTRACTThe subcellular localization of objects, such as organelles, proteins, or other molecules, instructs cellular form and function. Understanding the underlying spatial relationships between objects through colocalization analysis of microscopy images is a fundamental approach used to inform biological mechanisms. We generated an automated and customizable computational tool, the SubcellularDistribution pipeline, to facilitate object-based image analysis from three-dimensional (3D) fluorescence microcopy images. To test the utility of the SubcellularDistribution pipeline, we examined the subcellular distribution of mRNA relative to centrosomes within syncytial Drosophila embryos. Centrosomes are microtubule-organizing centers, and RNA enrichments at centrosomes are of emerging importance. Our open-source and freely available software detected RNA distributions comparably to commercially available image analysis software. The SubcellularDistribution pipeline is designed to guide the user through the complete process of preparing image analysis data for publication, from image segmentation and data processing to visualization.This article has an associated First Person interview with the first author of the paper.

scholarly journals CellProfiler™: free, versatile software for automated biological image analysis

BioTechniques ◽  
2007 ◽  
Vol 42 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Michael R. Lamprecht ◽  
David M. Sabatini ◽  
Anne E. Carpenter
Keyword(s):  
Image Analysis ◽  
Biological Image
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