scholarly journals Rosette Tracker: An Open Source Image Analysis Tool for Automatic Quantification of Genotype Effects

2012 ◽  
Vol 160 (3) ◽  
pp. 1149-1159 ◽  
Author(s):  
Jonas De Vylder ◽  
Filip Vandenbussche ◽  
Yuming Hu ◽  
Wilfried Philips ◽  
Dominique Van Der Straeten
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Source Image ◽  
Analysis Tool ◽  
Automatic Quantification ◽  
Genotype Effects

scholarly journals Orbit Image Analysis: An open-source whole slide image analysis tool

2019 ◽  
Author(s):  
Manuel Stritt ◽  
Anna K. Stalder ◽  
Enrico Vezzali
Keyword(s):  
Image Analysis ◽  
Distributed Computing ◽  
Open Source ◽  
Use Cases ◽  
Source Image ◽  
Complex Object ◽  
Analysis Tool ◽  
Whole Slide Image ◽  
Word Use ◽  
Slide Image

AbstractWe describe the open-source whole slide image analysis tool Orbit Image Analysis. It is a generic tile-processing engine which allows the execution of various image analysis algorithms provided by either Orbit itself or other open-source solutions using a tile-based map-reduce execution framework. We show its sophisticated machine-learning approach for WSI quantification, and its flexibility by integrating a deep learning segmentation method for complex object detection. It can run locally standalone or connect to the open-source image server OMERO, and provides scale-out functionality to use the Spark framework for distributed computing. We demonstrate the application of Orbit in three real-world use-cases: Idiopathic lung fibrosis, nerve fibre density quantification, and glomeruli detection in kidney.Author summaryWhole slide images (WSI) are digital scans of samples, e.g. tissue sections. It is very convenient to view samples in this digital form, and with the increasing computation power it can also be used for quantification. These images are often too large to be analysed with standard tools. To overcome this issue, we created on open-source tool called Orbit Image Analysis which divides the images into smaller parts and allows the analysis of it with either embedded algorithms or the integration of existing tools. It also provides mechanisms to process huge amounts of images in distributed computing environments such as clusters or cloud infrastructures. In this paper we describe the Orbit system and demonstrate its application based on three real-word use-cases.

scholarly journals EcoIP: An open source image analysis toolkit to identify different stages of plant phenology for multiple species with pan–tilt–zoom cameras

2013 ◽  
Vol 15 ◽  
pp. 58-65 ◽  
Author(s):  
Joel A. Granados ◽  
Eric A. Graham ◽  
Philippe Bonnet ◽  
Eric M. Yuen ◽  
Michael Hamilton
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Plant Phenology ◽  
Source Image ◽  
Multiple Species

CellStress - open source image analysis program for single-cell analysis

2010 ◽  
Author(s):  
Maria Smedh ◽  
Caroline Beck ◽  
Kristin Sott ◽  
Mattias Goksör
Keyword(s):  
Image Analysis ◽  
Single Cell ◽  
Open Source ◽  
Single Cell Analysis ◽  
Source Image ◽  
Cell Analysis ◽  
Analysis Program

scholarly journals NanoJ: a high-performance open-source super-resolution microscopy toolbox

2018 ◽  
Author(s):  
Romain F. Laine ◽  
Kalina L. Tosheva ◽  
Nils Gustafsson ◽  
Robert D. M. Gray ◽  
Pedro Almada ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
High Performance ◽  
Image Quality Assessment ◽  
Fluorescent Microscopy ◽  
Super Resolution ◽  
Quantitative Information ◽  
Ease Of Use ◽  
Source Image ◽  
Super Resolution Microscopy

Super-resolution microscopy has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for super-resolution microscopy designed to combine high performance and ease of use. We named it NanoJ - a reference to the popular ImageJ software it was de-veloped for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image re-construction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.

scholarly journals ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis

2018 ◽  
Vol 93 (7) ◽  
pp. 749-754
Author(s):  
Norbert Auer ◽  
Astrid Hrdina ◽  
Chaitra Hiremath ◽  
Sabine Vcelar ◽  
Martina Baumann ◽  
...  
Keyword(s):  
Image Analysis ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Open Source ◽  
Hybridization Analysis ◽  
Source Image ◽  
Analysis Software ◽  
Image Analysis Software ◽  
Multicolor Fluorescence

scholarly journals MATITK: EXTENDING MATLAB WITH ITK

2005 ◽  
Author(s):  
Vincent Chu ◽  
Ghassan Hamarneh
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Medical Image ◽  
Image Data ◽  
Source Image ◽  
Research Environment ◽  
Low Level ◽  
Medical Image Data

To facilitate the analysis of medical image data in research environment, MATITK is developed to allow ITK algorithms to be called in MATLAB. ITK is a powerful open-source image analysis toolkit, but it requires the knowledge of C++ to use it. With the help of MATITK, researchers familiar with MATLAB can harness the power of ITK without learning C++ and worrying about low-level programming issues. A common set of C++ classes have also been produced to allow future ITK methods to be added to MATITK therefore callable in MATLAB without the bothersome translation between MATLAB and ITK.

scholarly journals Orbit Image Analysis: An open-source whole slide image analysis tool

2020 ◽  
Vol 16 (2) ◽  
pp. e1007313 ◽  
Author(s):  
Manuel Stritt ◽  
Anna K. Stalder ◽  
Enrico Vezzali
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Analysis Tool ◽  
Whole Slide Image ◽  
Slide Image
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