scholarly journals Probelab ReImager: An Open-Source Software for Streamlining Image Processing in an Electron Microscopy Laboratory

2021 ◽  
Vol 29 (2) ◽  
pp. 38-41
Author(s):  
Noah Kraft ◽  
Anette von der Handt
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
Open Source ◽  
Open Source Software

scholarly journals Probelab ReImager: Open Source Software for Streamlining Image Processing

2020 ◽  
Vol 26 (S2) ◽  
pp. 2176-2177
Author(s):  
Noah Kraft ◽  
Anette von der Handt
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software

scholarly journals Electron Microscopy (Big and Small) Data Analysis With the Open Source Software Package HyperSpy

2017 ◽  
Vol 23 (S1) ◽  
pp. 214-215 ◽  
Author(s):  
Francisco de la Pena ◽  
Tomas Ostasevicius ◽  
Vidar Tonaas Fauske ◽  
Pierre Burdet ◽  
Petras Jokubauskas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Small Data ◽  
Open Source Software Package

scholarly journals ZebrafishMiner: an open source software for interactive evaluation of domain-specific fluorescence in zebrafish

2017 ◽  
Vol 3 (2) ◽  
pp. 199-202
Author(s):  
Markus Reischl ◽  
Andreas Bartschat ◽  
Urban Liebel ◽  
Jochen Gehrig ◽  
Ference Müller ◽  
...  
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Drug Effects ◽  
Processing Parameters ◽  
Domain Specific ◽  
Processing Pipeline ◽  
Open Source Software Package ◽  
Programming Knowledge

AbstractHigh-throughput microscopy makes it possible to observe the morphology of zebrafish on large scale to quantify genetic, toxic or drug effects. The image acquisition is done by automated microscopy, images are evaluated automatically by image processing pipelines, tailored specifically to the requirements of the scientific question. The transfer of such algorithms to other projects, however, is complex due to missing guidelines and lack of mathematical or programming knowledge. In this work, we implement an image processing pipeline for automatic fluorescence quantification in user-defined domains of zebrafish embryos and larvae of different age. The pipeline is capable of detecting embryos and larvae in image stacks and quantifying domain activity. To make this protocol available to the community, we developed an open source software package called „ZebrafishMiner“ which guides the user through all steps of the processing pipeline and makes the algorithms available and easy to handle. We implemented all routines in an MATLAB-based graphical user interface (GUI) that gives the user control over all image processing parameters. The software is shipped with a manual of 30 pages and three tutorial datasets, which guide the user through the manual step by step. It can be downloaded at https://sourceforge.net/projects/scixminer/.

scholarly journals Image Processing Filters for Grids of Cells Analogous to Filters Processing Grids of Pixels

2021 ◽  
Vol 3 ◽  
Author(s):  
Robert Haase
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software ◽  
Image Data ◽  
Tissue Level ◽  
General Purpose ◽  
Cellular Processes ◽  
Microscopy Image ◽  
Programming Skills ◽  
User Friendly

Intra- and extra-cellular processes shape tissues together. For understanding how neighborhood relationships between cells play a role in this process, having image processing filters based on these relationships would be beneficial. Those operations are known and their application to microscopy image data typically requires programming skills. User-friendly general purpose tools for pursuing image processing on a level of neighboring cells were yet missing. In this manuscript I demonstrate image processing filters which process grids of cells on tissue level and the analogy to their better known counter parts processing grids of pixels. The tools are available as part of free and open source software in the ImageJ/Fiji and napari ecosystems and their application does not require any programming experience.

Open source software for medical image processing and visualization

2005 ◽  
Vol 48 (2) ◽  
pp. 55-59 ◽  
Author(s):  
Terry S. Yoo ◽  
Michael J. Ackerman
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software ◽  
Medical Image ◽  
Medical Image Processing

scholarly journals BLOB Analysis for Fruit Recognition and Detection

2018 ◽  
Vol 7 (1) ◽  
pp. 25-36 ◽  
Author(s):  
Muhammad Dede Yusuf ◽  
RD Kusumanto ◽  
Yurni Oktarina ◽  
Tresna Dewi ◽  
Pola Risma
Keyword(s):  
Image Processing ◽  
Object Detection ◽  
Open Source ◽  
Open Source Software ◽  
Image Sensor ◽  
Blob Analysis ◽  
Different Shapes ◽  
Simulation Results ◽  
Short Time ◽  
Harvesting Robot

Robot application in agriculture can ease the farming process, especially as the harvesting robot for seasonal fruit that is available in a short time. The addition of "eye" as the image sensor is an important feature for a harvesting robot. Thanks to the increment of technology, the camera is getting smaller with better performance, and lower prices. The cheap sensors and components make the creation of cheap and effective robot possible. Image processing is necessary for object detection, and open source software is available now for this purpose. This paper proposes BLOB analysis for object detection of 5 fruits with different shapes and colors. The simulation results show that the proposed method is effective for object detection regardless the shapes, colors, and noises.

Image Processing for Micro UAV with Open Source Software

2016 ◽  
Vol 16 (3) ◽  
pp. 139-151
Author(s):  
Ilyoung Hong ◽  
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software
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