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Journal Articles

VISION – an open-source software for automated multi-dimensional image analysis of cellular biophysics

Open Access
In collection:
Imaging
Florian Weber, Sofiia Iskrak, Franziska Ragaller, Jan Schlegel, Birgit Plochberger, Erdinc Sezgin, Luca A. Andronico
Journal: Journal of Cell Science
J Cell Sci (2024) 137 (20): jcs262166.
https://doi.org/10.1242/jcs.262166
Published: 23 October 2024
...Florian Weber; Sofiia Iskrak; Franziska Ragaller; Jan Schlegel; Birgit Plochberger; Erdinc Sezgin; Luca A. Andronico ABSTRACT Environment-sensitive probes are frequently used in spectral and multi-channel microscopy to study alterations in cell homeostasis. However, the few open-source packages...
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Includes: Supplementary data
Journal Articles

GIANI – open-source software for automated analysis of 3D microscopy images

Open Access
In collection:
Imaging
David J. Barry, Claudia Gerri, Donald M. Bell, Rocco D'Antuono, Kathy K. Niakan
Journal: Journal of Cell Science
J Cell Sci (2022) 135 (10): jcs259511.
https://doi.org/10.1242/jcs.259511
Published: 17 May 2022
...-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a limited number of open-source software packages to analyse such images. Here, we describe General Image Analysis of Nuclei-based Images (GIANI; https://djpbarry.github.io/Giani), new software...
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Includes: Supplementary data
Journal Articles

Deep learning ­– promises for 3D nuclear imaging: a guide for biologists

Open Access
In collection:
Imaging , Nuclear structure and function
Guillaume Mougeot, Tristan Dubos, Frédéric Chausse, Emilie Péry, Katja Graumann, Christophe Tatout, David E. Evans, Sophie Desset
Journal: Journal of Cell Science
J Cell Sci (2022) 135 (7): jcs258986.
https://doi.org/10.1242/jcs.258986
Published: 14 April 2022
... interdisciplinary research between computer scientists and biologists. 3D nucleus Deep learning 3D microscopy images 3D segmentation Image dataset Open source Centre National de la Recherche Scientifique http://dx.doi.org/10.13039/501100004794 Institut National de la Santé et de la...
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Includes: Supplementary data
Journal Articles

Python-Microscope – a new open-source Python library for the control of microscopes

Open Access
In collection:
Imaging
David Miguel Susano Pinto, Mick A. Phillips, Nicholas Hall, Julio Mateos-Langerak, Danail Stoychev, Tiago Susano Pinto, Martin J. Booth, Ilan Davis, Ian M. Dobbie
Journal: Journal of Cell Science
J Cell Sci (2021) 134 (19): jcs258955.
https://doi.org/10.1242/jcs.258955
Published: 6 October 2021
... desirable to have a solution that is scalable to complex systems and that is translatable between components from different manufacturers. Here we report Python-Microscope, a free and open-source Python library for high-performance control of arbitrarily complex and scalable custom microscope systems...
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Includes: Supplementary data