15 results on '"Charles N. Christensen"'
Search Results
2. Calcium imaging analysis – how far have we come? [version 2; peer review: 1 approved, 2 approved with reservations]
- Author
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Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, and Marta Zlatic
- Subjects
Medicine ,Science - Abstract
Techniques for calcium imaging were first demonstrated in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved today. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.
- Published
- 2021
- Full Text
- View/download PDF
3. Spatio-temporal Vision Transformer for Super-resolution Microscopy.
- Author
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Charles N. Christensen, Meng Lu, Edward N. Ward, Pietro Liò, and Clemens F. Kaminski
- Published
- 2022
- Full Text
- View/download PDF
4. Calcium imaging analysis – how far have we come? [version 2; peer review: 3 approved]
- Author
-
Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, and Marta Zlatic
- Subjects
Review ,Articles ,Calcium Imaging ,Denoising ,Motion Correction ,Classification ,Quantification ,Machine Learning ,Neural Networks - Abstract
Techniques for calcium imaging were first demonstrated in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved today. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.
- Published
- 2021
- Full Text
- View/download PDF
5. Calcium imaging analysis – how far have we come? [version 1; peer review: 3 approved with reservations]
- Author
-
Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, and Marta Zlatic
- Subjects
Review ,Articles ,Calcium Imaging ,Denoising ,Motion Correction ,Classification ,Quantification ,Machine Learning ,Neural Networks - Abstract
Techniques for calcium imaging were first achieved in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular, alongside our preferred, methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress, and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.
- Published
- 2021
- Full Text
- View/download PDF
6. ML-SIM: A deep neural network for reconstruction of structured illumination microscopy images.
- Author
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Charles N. Christensen, Edward N. Ward, Pietro Lió, and Clemens F. Kaminski
- Published
- 2020
7. Spatial Variation of Fine Particulate Matter Levels in Nairobi Before and During the COVID-19 Curfew: Implications for Environmental Justice
- Author
-
Priyanka N deSouza, Phoebe Atsieno Oriama, Peter P Pedersen, Sebastian Horstmann, Lorena Gordillo-Dagallier, Charles N Christensen, Christoph O Franck, Richard Ayah, Ralph A Kahn, Jacqueline M Klopp, Kyle P Messier, and Patrick L Kinney
- Subjects
Environment Pollution - Abstract
The temporary decrease of fine particulate matter (PM(sub 2.5)) concentrations in many parts of the world due to the COVID-19 lockdown spurred discussions on urban air pollution and health. However there has been little focus on sub-Saharan Africa, as few African cities have air quality monitors and if they do, these data are often not publicly available. Spatial differentials of changes in PM(sub 2.5) concentrations as a result of COVID also remain largely unstudied. To address this gap, we use a serendipitous mobile air quality monitoring deployment of eight Sensirion SPS 30 sensors on motorbikes in the city of Nairobi starting on 16 March 2020, before a COVID-19 curfew was imposed on 25 March and continuing until 5 May 2020. We developed a random-forest model to estimate PM(sub 2.5) surfaces for the entire city of Nairobi before and during the COVID-19 curfew. The highest PM(sub 2.5) concentrations during both periods were observed in the poor neighborhoods of Kariobangi, Mathare, Umoja, and Dandora, located to the east of the city center. Changes in PM(sub 2.5) were heterogeneous over space. PM(sub 2.5) concentrations increased during the curfew in rapidly urbanizing, the lower-middle-class neighborhoods of Kahawa, Kasarani, and Ruaraka, likely because residents switched from LPG to biomass fuels due to loss of income. Our results indicate that COVID-19 and policies to address it may have exacerbated existing air pollution inequalities in the city of Nairobi. The quantitative results are preliminary, due to sampling limitations and measurement uncertainties, as the available data came exclusively from low-cost sensors. This research serves to highlight that spatial data that is essential for understanding structural inequalities reflected in uneven air pollution burdens and differential impacts of events like the COVID pandemic. With the help of carefully deployed low cost sensors with improved spatial sampling and at least one reference-quality monitor for calibration, we can collect data that is critical for developing targeted interventions that address environmental injustice in the African context.
- Published
- 2021
- Full Text
- View/download PDF
8. ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology
- Author
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Meng Lu, Charles N. Christensen, Jana M. Weber, Tasuku Konno, Nino F. Läubli, Katharina M. Scherer, Edward Avezov, Pietro Lio, Alexei A. Lapkin, Gabriele S. Kaminski Schierle, Clemens F. Kaminski, Weber, Jana M [0000-0002-2867-0087], Läubli, Nino F [0000-0003-2894-2385], Lapkin, Alexei A [0000-0001-7621-0889], Kaminski Schierle, Gabriele S [0000-0002-1843-2202], Kaminski, Clemens F [0000-0002-5194-0962], and Apollo - University of Cambridge Repository
- Subjects
Cell Biology ,Endoplasmic Reticulum ,Molecular Biology ,Biochemistry ,Biotechnology ,Semantics - Abstract
The ability to quantify structural changes of the endoplasmic reticulum (ER) is crucial for understanding the structure and function of this organelle. However, the rapid movement and complex topology of ER networks make this challenging. Here, we construct a state-of-the-art semantic segmentation method that we call ERnet for the automatic classification of sheet and tubular ER domains inside individual cells. Data are skeletonized and represented by connectivity graphs, enabling precise and efficient quantification of network connectivity. ERnet generates metrics on topology and integrity of ER structures and quantifies structural change in response to genetic or metabolic manipulation. We validate ERnet using data obtained by various ER-imaging methods from different cell types as well as ground truth images of synthetic ER structures. ERnet can be deployed in an automatic high-throughput and unbiased fashion and identifies subtle changes in ER phenotypes that may inform on disease progression and response to therapy.
- Published
- 2023
- Full Text
- View/download PDF
9. ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology for video-rate super-resolution imaging
- Author
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Meng Lu, Charles N. Christensen, Jana M. Weber, Tasuku Konno, Nino F. Läubli, Katharina M. Scherer, Edward Avezov, Pietro Lio, Alexei A. Lapkin, Gabriele S. Kaminski Schierle, and Clemens F. Kaminski
- Abstract
The topology of endoplasmic reticulum (ER) network is highly regulated by various cellular and environmental stimuli and affects major functions such as protein quality control and the cell’s response to metabolic changes. The ability to quantify the dynamical changes of the ER structures in response to cellular perturbations is crucial for the development of novel therapeutic approaches against ER associated diseases, such as hereditary spastic paraplegias and Niemann Pick Disease type C. However, the rapid movement and small spatial dimension of ER networks make this task challenging. Here, we combine video-rate super-resolution imaging with a state-of-the-art semantic segmentation method capable of automatically classifying sheet and tubular ER domains inside individual cells. Data are skeletonised and represented by connectivity graphs to enable the precise and efficient quantification and comparison of the network connectivity from different complex ER phenotypes. The method, called ERnet, is powered by a Vision Transformer architecture, and integrates multi-head self-attention and channel attention into the model for adaptive weighting of frames in the time domain. We validated the performance of ERnet by measuring different ER morphology changes in response to genetic or metabolic manipulations. Finally, as a means to test the applicability and versatility of ERnet, we showed that ERnet can be applied to images from different cell types and also taken from different imaging setups. Our method can be deployed in an automatic, high-throughput, and unbiased fashion to identify subtle changes in cellular phenotypes that can be used as potential diagnostics for propensity to ER mediated disease, for disease progression, and for response to therapy.
- Published
- 2022
10. ML-SIM: universal reconstruction of structured illumination microscopy images using transfer learning
- Author
-
Charles N. Christensen, Meng Lu, Pietro Liò, Edward Ward, Clemens F. Kaminski, Christensen, Charles N [0000-0002-5355-1063], and Apollo - University of Cambridge Repository
- Subjects
0303 health sciences ,Source code ,Image quality ,Computer science ,business.industry ,media_common.quotation_subject ,Graphics processing unit ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,01 natural sciences ,Sample (graphics) ,Atomic and Molecular Physics, and Optics ,Article ,010309 optics ,03 medical and health sciences ,Software ,Robustness (computer science) ,0103 physical sciences ,Computer vision ,Artificial intelligence ,Noise (video) ,business ,Image resolution ,030304 developmental biology ,Biotechnology ,media_common - Abstract
Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible with live-cell imaging. However, the reconstruction of SIM images is often slow, prone to artefacts, and requires multiple parameter adjustments to reflect different hardware or experimental conditions. Here, we introduce a versatile reconstruction method, ML-SIM, which makes use of transfer learning to obtain a parameter-free model that generalises beyond the task of reconstructing data recorded by a specific imaging system for a specific sample type. We demonstrate the generality of the model and the high quality of the obtained reconstructions by application of ML-SIM on raw data obtained for multiple sample types acquired on distinct SIM microscopes. ML-SIM is an end-to-end deep residual neural network that is trained on an auxiliary domain consisting of simulated images, but is transferable to the target task of reconstructing experimental SIM images. By generating the training data to reflect challenging imaging conditions encountered in real systems, ML-SIM becomes robust to noise and irregularities in the illumination patterns of the raw SIM input frames. Since ML-SIM does not require the acquisition of experimental training data, the method can be efficiently adapted to any specific experimental SIM implementation. We compare the reconstruction quality enabled by ML-SIM with current state-of-the-art SIM reconstruction methods and demonstrate advantages in terms of generality and robustness to noise for both simulated and experimental inputs, thus making ML-SIM a useful alternative to traditional methods for challenging imaging conditions. Additionally, reconstruction of a SIM stack is accomplished in less than 200 ms on a modern graphics processing unit, enabling future applications for real-time imaging. Source code and ready-to-use software for the method are available at http://ML-SIM.github.io.
- Published
- 2020
11. The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes
- Author
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David Holcman, Charles N. Christensen, Christine E. Holt, Lukas C. Kapitein, Pierre Parutto, Francesca W. van Tartwijk, Gabriele Kaminski Schierle, Edward Avezov, Julie Qiaojin Lin, Wilco Nijenhuis, Alan Tunnacliffe, Clemens F. Kaminski, Marcus Fantham, Meng Lu, Lu, Meng [0000-0001-9311-2666], van Tartwijk, Francesca [0000-0002-9795-2571], Lin, Qiaojin [0000-0002-2669-6478], Christensen, Charles [0000-0002-5355-1063], Avezov, Edward [0000-0002-2894-0585], Holt, Christine [0000-0003-2829-121X], Kaminski Schierle, Gabriele [0000-0002-1843-2202], Kaminski, Clemens [0000-0002-5194-0962], and Apollo - University of Cambridge Repository
- Subjects
Chemistry ,Endoplasmic reticulum ,Cell ,Metabolic change ,Nutritional status ,3101 Biochemistry and Cell Biology ,Cell biology ,medicine.anatomical_structure ,Tubule ,Global distribution ,Lysosome ,medicine ,Causal link ,health care economics and organizations ,31 Biological Sciences - Abstract
The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling within minutes are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status. The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. Lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.
- Published
- 2020
12. Spatial variation of fine particulate matter levels in Nairobi before and during the COVID-19 curfew: implications for environmental justice
- Author
-
Charles N. Christensen, Lorena Gordillo-Dagallier, Christoph O. Franck, Ralph A. Kahn, Richard Ayah, Patrick L. Kinney, Kyle P. Messier, Sebastian Horstmann, Priyanka deSouza, P. P. Pedersen, Jacqueline M. Klopp, and Phoebe Atsieno Oriama
- Subjects
Environmental justice ,Atmospheric Science ,Inequality ,media_common.quotation_subject ,Air pollution ,Geology ,Context (language use) ,Particulates ,medicine.disease_cause ,Agricultural and Biological Sciences (miscellaneous) ,Geography ,medicine ,Spatial variability ,Curfew ,Air quality index ,Environmental planning ,Earth-Surface Processes ,General Environmental Science ,Food Science ,media_common - Abstract
The temporary decrease of fine particulate matter (PM2.5) concentrations in many parts of the world due to the COVID-19 lockdown spurred discussions on urban air pollution and health. However there has been little focus on sub-Saharan Africa, as few African cities have air quality monitors and if they do, these data are often not publicly available. Spatial differentials of changes in PM2.5 concentrations as a result of COVID also remain largely unstudied. To address this gap, we use a serendipitous mobile air quality monitoring deployment of eight Sensirion SPS 30 sensors on motorbikes in the city of Nairobi starting on 16 March 2020, before a COVID-19 curfew was imposed on 25 March and continuing until 5 May 2020. We developed a random-forest model to estimate PM2.5 surfaces for the entire city of Nairobi before and during the COVID-19 curfew. The highest PM2.5 concentrations during both periods were observed in the poor neighborhoods of Kariobangi, Mathare, Umoja, and Dandora, located to the east of the city center. Changes in PM2.5 were heterogeneous over space. PM2.5 concentrations increased during the curfew in rapidly urbanizing, the lower-middle-class neighborhoods of Kahawa, Kasarani, and Ruaraka, likely because residents switched from LPG to biomass fuels due to loss of income. Our results indicate that COVID-19 and policies to address it may have exacerbated existing air pollution inequalities in the city of Nairobi. The quantitative results are preliminary, due to sampling limitations and measurement uncertainties, as the available data came exclusively from low-cost sensors. This research serves to highlight that spatial data that is essential for understanding structural inequalities reflected in uneven air pollution burdens and differential impacts of events like the COVID pandemic. With the help of carefully deployed low-cost sensors with improved spatial sampling and at least one reference-quality monitor for calibration, we can collect data that is critical for developing targeted interventions that address environmental injustice in the African context.
- Published
- 2021
13. Calcium imaging analysis – how far have we come?
- Author
-
Clemens F. Kaminski, Charles N. Christensen, Marta Zlatic, Miranda Robbins, Robbins, Miranda [0000-0002-6576-5763], and Apollo - University of Cambridge Repository
- Subjects
Diagnostic Imaging ,0301 basic medicine ,Cellular activity ,Neural Networks ,Computer science ,Motion Correction ,Review ,General Biochemistry, Genetics and Molecular Biology ,Machine Learning ,03 medical and health sciences ,Calcium imaging ,0302 clinical medicine ,Quantification ,Image Processing, Computer-Assisted ,General Pharmacology, Toxicology and Pharmaceutics ,Denoising ,General Immunology and Microbiology ,Articles ,General Medicine ,Motion correction ,Classification ,Data science ,Calcium Imaging ,030104 developmental biology ,Calcium ,030217 neurology & neurosurgery - Abstract
Techniques for calcium imaging were first achieved in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular, alongside our preferred, methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress, and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.
- Published
- 2021
14. Driving-induced population trapping and linewidth narrowing via the quantum Zeno effect
- Author
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Dara P. S. McCutcheon, Charles N. Christensen, Jesper Mørk, Jake Iles-Smith, and Torkil S. Petersen
- Subjects
Population ,Physics::Optics ,FOS: Physical sciences ,02 engineering and technology ,01 natural sciences ,law.invention ,Laser linewidth ,QETLabs ,law ,0103 physical sciences ,Spontaneous emission ,Emission spectrum ,010306 general physics ,education ,Quantum ,Quantum Zeno effect ,Physics ,Quantum Physics ,education.field_of_study ,Observable ,021001 nanoscience & nanotechnology ,Optical cavity ,Quantum electrodynamics ,0210 nano-technology ,Quantum Physics (quant-ph) - Abstract
We investigate the suppression of spontaneous emission from a driven three-level system embedded in an optical cavity via a manifestation of the quantum Zeno effect. Strong resonant coupling of the lower two levels to an external optical field results in a decrease of the decay rate of the third upper level. We show that this effect has observable consequences in the form of emission spectra with subnatural linewidths, which should be measurable using, for example, quantum dot-cavity systems in currently obtainable parameter regimes, and may find use in applications requiring the control of single-photon arrival times and wave-packet extent. These results suggest an underappreciated link between the Zeno effect, dressed states, and Purcell enhancement.
- Published
- 2017
- Full Text
- View/download PDF
15. REACTIONS TO POLIOMYELITIS VACCINE
- Author
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Charles N. Christensen
- Subjects
Local pain ,Poliomyelitis vaccine ,Vaccines ,Allergy ,Pediatrics ,medicine.medical_specialty ,business.industry ,Incidence (epidemiology) ,Prevalence ,medicine.disease ,Poliomyelitis ,Immunology ,medicine ,Anaphylactoid reactions ,business - Abstract
Complaints received by a manufacturer from physicians concerning unfavorable reactions to formaldehyde-inactivated poliomyelitis vaccine have been analyzed. The use of 184,000,000 doses of vaccine was followed by 284 complaints, of which 138 concerned only stinging or burning local pain. In six instances the symptoms suggested poliomyelitis, but in no case were the three essential criteria of inoculation-induced poliomyelitis satisfied. The most severe reactions reported in connection with this vaccine were four anaphylactoid reactions, and in each case recovery was complete. The most frequent types of reaction were allergic (56 cases) and neurological (37). The complaint rate was therefore extremely low, and the relative safety of the vaccine was apparent.
- Published
- 1959
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