J. Savatier - Academia.edu (original) (raw)
Papers by J. Savatier
Videomicrofluorometry on living cells and discriminant factorial analysis to study cell cycle dis... more Videomicrofluorometry on living cells and discriminant factorial analysis to study cell cycle distributions
Journal of biological regulators and homeostatic agents, 2004
After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging ... more After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging microscopy method is proposed. This method is improved by a factorial analysis relying on the evaluation of several parameters recorded on each living cell. Single lympho-blastoid living cells are labeled with three fluorescent markers: Hoechst 33342 for nuclear DNA, Rhodamine 123 for mitochondria and Nile Red for plasma membrane. For each cell, morphological and functional information parameters are obtained. A typological analysis is used to separate control cells into four groups: G0-G1, S, G2+M and polyploid cells Gn. These control cells define a learning population used to analyze untreated and adriamycine treated cells as supplementary individuals in a discriminant factorial analysis. Such an approach allows to accurately evidence the change of the values of some cellular parameters.
In this supplementary information, we describe the blind-SIM (for blind Structured Illumination M... more In this supplementary information, we describe the blind-SIM (for blind Structured Illumination Microscopy) algorithm that is able to estimate the sample fluorescence density from low resolution images obtained under unknown excitation patterns. We provide a numerical study of its performance with respect to noise and compare it to classical periodic SIM with known excitation patterns. Last, we apply it to simulated periodic SIM data in which the periodic excitation patterns are strongly distorted.
Biomedical Optics Express
The quantitative phase imaging methods have several advantages when it comes to monitoring cultur... more The quantitative phase imaging methods have several advantages when it comes to monitoring cultures of adherent mammalian cells. Because of low photo-toxicity and no need for staining, we can follow cells in a minimally invasive way over a long period of time. The ability to measure the optical path difference in a quantitative manner allows the measurement of the cell dry mass, an important metric for studying the growth kinetics of mammalian cells. Here we present and compare cell measurements obtained with three different techniques: digital holographic microscopy, lens-free microscopy and quadriwave lateral sheering interferometry. We report a linear relationship between optical volume density values measured with these different techniques and estimate the precisions of this measurement for the different individual instruments.
2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, 2013
ABSTRACT Biomolecular orientational organization is an important parameter in biological processe... more ABSTRACT Biomolecular orientational organization is an important parameter in biological processes where functions (such as cell motility, vesicular trafficking, signalling, protein interactions, etc.) are closely related to orientation and ordering. The investigation of structural behaviors is today a determining factor for a better understanding of fundamental mechanisms governing cell membranes and proteins assemblies, which is particularly relevant for instance in neuro-degenerative diseases related to proteins aggregates formation.
Biophysical Journal, 2014
Journal of biological regulators and homeostatic agents
After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging ... more After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging microscopy method is proposed. This method is improved by a factorial analysis relying on the evaluation of several parameters recorded on each living cell. Single lympho-blastoid living cells are labeled with three fluorescent markers: Hoechst 33342 for nuclear DNA, Rhodamine 123 for mitochondria and Nile Red for plasma membrane. For each cell, morphological and functional information parameters are obtained. A typological analysis is used to separate control cells into four groups: G0-G1, S, G2+M and polyploid cells Gn. These control cells define a learning population used to analyze untreated and adriamycine treated cells as supplementary individuals in a discriminant factorial analysis. Such an approach allows to accurately evidence the change of the values of some cellular parameters.
1. ABSTRACT In Structured Illumination Microscopy (SIM) the fluorescent samples are illuminated w... more 1. ABSTRACT In Structured Illumination Microscopy (SIM) the fluorescent samples are illuminated with periodic light patterns in order to obtain an improvement of the resolution beyond the diffraction-limited detection band pass [1-3]. The distribution of fluorophores is determined with a reconstruction process that assumes a precise knowledge of the illumination grid. For this reason, SIM is sensitive to aberrations, to mechanical and thermal drifts of the setup. Recently, a technique called blind-SIM [4] has shown, both theoretically and experimentally, that the image reconstruction can be performed even when the samples are illuminated with random unknown light patterns, provided that their average is almost homogeneous over the sample. Results have been presented when the samples are illuminated by a set of speckle patterns and when an iterative algorithm of reconstruction based on the resolution of an inverse problem is used for retrieving the distribution of fluorophores. We will show that the method of reconstruction developed for the blind-SIM can be modified and adapted in order to recover the distribution of fluorophores from the data given by standard SIM setups. The advantage in this case is that the reconstructions are insensitive to the distortions of the light grid produced by lens aberrations, misalignements or phase shifting errors. We present numerical and experimental results obtained when deformed light grids are projected on the samples. We analyze the robustness of the technique against aberrations, phase shifting errors and noise.
ABSTRACT Biomolecular orientational organization is an important parameter in biological processe... more ABSTRACT Biomolecular orientational organization is an important parameter in biological processes where functions (such as cell motility, vesicular trafficking, signalling, protein interactions, etc.) are closely related to orientation and ordering. The investigation of structural behaviors is today a determining factor for a better understanding of fundamental mechanisms governing cell membranes and proteins assemblies, which is particularly relevant for instance in neuro-degenerative diseases related to proteins aggregates formation.
Videomicrofluorometry on living cells and discriminant factorial analysis to study cell cycle dis... more Videomicrofluorometry on living cells and discriminant factorial analysis to study cell cycle distributions
Journal of biological regulators and homeostatic agents, 2004
After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging ... more After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging microscopy method is proposed. This method is improved by a factorial analysis relying on the evaluation of several parameters recorded on each living cell. Single lympho-blastoid living cells are labeled with three fluorescent markers: Hoechst 33342 for nuclear DNA, Rhodamine 123 for mitochondria and Nile Red for plasma membrane. For each cell, morphological and functional information parameters are obtained. A typological analysis is used to separate control cells into four groups: G0-G1, S, G2+M and polyploid cells Gn. These control cells define a learning population used to analyze untreated and adriamycine treated cells as supplementary individuals in a discriminant factorial analysis. Such an approach allows to accurately evidence the change of the values of some cellular parameters.
In this supplementary information, we describe the blind-SIM (for blind Structured Illumination M... more In this supplementary information, we describe the blind-SIM (for blind Structured Illumination Microscopy) algorithm that is able to estimate the sample fluorescence density from low resolution images obtained under unknown excitation patterns. We provide a numerical study of its performance with respect to noise and compare it to classical periodic SIM with known excitation patterns. Last, we apply it to simulated periodic SIM data in which the periodic excitation patterns are strongly distorted.
Biomedical Optics Express
The quantitative phase imaging methods have several advantages when it comes to monitoring cultur... more The quantitative phase imaging methods have several advantages when it comes to monitoring cultures of adherent mammalian cells. Because of low photo-toxicity and no need for staining, we can follow cells in a minimally invasive way over a long period of time. The ability to measure the optical path difference in a quantitative manner allows the measurement of the cell dry mass, an important metric for studying the growth kinetics of mammalian cells. Here we present and compare cell measurements obtained with three different techniques: digital holographic microscopy, lens-free microscopy and quadriwave lateral sheering interferometry. We report a linear relationship between optical volume density values measured with these different techniques and estimate the precisions of this measurement for the different individual instruments.
2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, 2013
ABSTRACT Biomolecular orientational organization is an important parameter in biological processe... more ABSTRACT Biomolecular orientational organization is an important parameter in biological processes where functions (such as cell motility, vesicular trafficking, signalling, protein interactions, etc.) are closely related to orientation and ordering. The investigation of structural behaviors is today a determining factor for a better understanding of fundamental mechanisms governing cell membranes and proteins assemblies, which is particularly relevant for instance in neuro-degenerative diseases related to proteins aggregates formation.
Biophysical Journal, 2014
Journal of biological regulators and homeostatic agents
After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging ... more After a rapid overview of the approaches used to study cell cycle, a fluorescent digital imaging microscopy method is proposed. This method is improved by a factorial analysis relying on the evaluation of several parameters recorded on each living cell. Single lympho-blastoid living cells are labeled with three fluorescent markers: Hoechst 33342 for nuclear DNA, Rhodamine 123 for mitochondria and Nile Red for plasma membrane. For each cell, morphological and functional information parameters are obtained. A typological analysis is used to separate control cells into four groups: G0-G1, S, G2+M and polyploid cells Gn. These control cells define a learning population used to analyze untreated and adriamycine treated cells as supplementary individuals in a discriminant factorial analysis. Such an approach allows to accurately evidence the change of the values of some cellular parameters.
1. ABSTRACT In Structured Illumination Microscopy (SIM) the fluorescent samples are illuminated w... more 1. ABSTRACT In Structured Illumination Microscopy (SIM) the fluorescent samples are illuminated with periodic light patterns in order to obtain an improvement of the resolution beyond the diffraction-limited detection band pass [1-3]. The distribution of fluorophores is determined with a reconstruction process that assumes a precise knowledge of the illumination grid. For this reason, SIM is sensitive to aberrations, to mechanical and thermal drifts of the setup. Recently, a technique called blind-SIM [4] has shown, both theoretically and experimentally, that the image reconstruction can be performed even when the samples are illuminated with random unknown light patterns, provided that their average is almost homogeneous over the sample. Results have been presented when the samples are illuminated by a set of speckle patterns and when an iterative algorithm of reconstruction based on the resolution of an inverse problem is used for retrieving the distribution of fluorophores. We will show that the method of reconstruction developed for the blind-SIM can be modified and adapted in order to recover the distribution of fluorophores from the data given by standard SIM setups. The advantage in this case is that the reconstructions are insensitive to the distortions of the light grid produced by lens aberrations, misalignements or phase shifting errors. We present numerical and experimental results obtained when deformed light grids are projected on the samples. We analyze the robustness of the technique against aberrations, phase shifting errors and noise.
ABSTRACT Biomolecular orientational organization is an important parameter in biological processe... more ABSTRACT Biomolecular orientational organization is an important parameter in biological processes where functions (such as cell motility, vesicular trafficking, signalling, protein interactions, etc.) are closely related to orientation and ordering. The investigation of structural behaviors is today a determining factor for a better understanding of fundamental mechanisms governing cell membranes and proteins assemblies, which is particularly relevant for instance in neuro-degenerative diseases related to proteins aggregates formation.