Bio-friendly long-term subcellular dynamic recording by self-supervised image enhancement microscopy
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- Evaluated articles (Arcadia Science)
Abstract
Fluorescence microscopy has become an indispensable tool for revealing the dynamic regulation of cells and organelles. However, stochastic noise inherently restricts optical interrogation quality and exacerbates observation fidelity when balancing the joint demands of high frame rate, long-term recording and low phototoxicity. Here we propose DeepSeMi, a self-supervised-learning-based denoising framework capable of increasing signal-to-noise ratio by over 12 dB across various conditions. With the introduction of newly designed eccentric blind-spot convolution filters, DeepSeMi effectively denoises images with no loss of spatiotemporal resolution. In combination with confocal microscopy, DeepSeMi allows for recording organelle interactions in four colors at high frame rates across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames. Through comprehensive validations across various samples and instruments, we prove DeepSeMi to be a versatile and biocompatible tool for breaking the shot-noise limit.
Article activity feed
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A very interesting computer-learning technique to improve signal to noise and enhance resolution of sub-cellular structures. The impact of this work will be more directly transmitted with clearer writing. Some specific suggestions are annotated throughout the paper.
One tool that might facilitate this is: https://hemingwayapp.com/
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bonds
should this be "bounds"?
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efficacious
perhaps "effective" is more direct
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requiring no clean data as references and no compromise of spatiotemporal resolution on diverse imaging systems
without the need for baseline data or loss of spatiotemporal resolution
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The computationally 15-fold multiplied photon budget in a standard confocal microscope by DeepSeMi allows for recording organelle interactions in four colors and high-frame-rate across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames, all faithfully and sample-friendly.
consider making this a simpler, declarative statement(s)
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confocal microscope,
may want to specify the type of confocal here in addition to the methods.
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higher NA objective suffers even more from scattering
can you clarify how an objective with increased resolution (higher NA) leads to more scattering?
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generality
generalizability might be better here
-
all faithfully
awkward phrasing
-
to be
should be "from being"
-
enlarged
increased is a better word choice than enlarged. Enlarged means to make bigger in size not magnitude. Increased is more accurate when talking about a larger number.
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clean data
more precise to say "data with high SNR"?
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and bio-friendly breaking the shot-noise limit, facilitating automated analysis of massive data about cell migrations and organelle interactions.
simplify and make more direct
-
brand-
can eliminate to reduce redundancy
-
fluctuated
what does fluctuated mean here?
-
Besides,
Eliminate this.
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the contamination inevitable
specify the type of contamination
-
roots in
odd phrasing here. What is more direct verb that can be used here?
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Fig. 4
Excellent figure to demonstrate the improvement in resolution with DeepSeMi over the raw images.
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no-compromise results
can no-compromise results be defined clearly?
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commercial
what kind?
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ten folds
tenfold
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DeepSeMi
Use of DeepSeMi
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colors
suggest saying "fluorophores in different channels. They were: tagBFP-SKL (Ex/Em 402/457 nm),..." to give the excitation and emission spectra for each fluorophore.
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in nonlinear microscope
using nonlinear microscopy or with a nonlinear microscope (and then specify which type)
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dye concentration
which dye concentration was better?
-
enlarging excitation dosage
"increasing laser power" ?
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brittle
what does brittle mean here?
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magnificence of the harmonically orchestrated systems, organs, tissues, and cells
awkward phrasing. Perhaps something like "magnificently well-orchestrated systems of organs, tissues, and cells" or
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vehemently enlarged
"drastically improved" would be better
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Compared to recently developed interpolation-based denoising methods, DeepSeMi is capable of observing organelles of sophisticated movements and transformations without motion artifacts
Great point, may be stronger if framed as, "DeepSeMi improves upon interpolation-based denoising methods by (fill in the blank to describe what it is based on), which allows for observation of organelle dynamics without motion artifacts"
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high-frame-rate
revise use of hypens throughout. three hyphens should not be used consecutively.
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lustrous and remarkable advances in enriched fluorescence microscope[1, 9–12] have brought flourishing discoveries
awkward phrasing. Not sure what "enriched fluorescence microscope" really means
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100 ×
100x
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36,000 shots in multicolor
not a standard way to report this.
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Excitation power was set at 2% t
for which laser?
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Such gorgeous patterns reflect live organelles of complex, dynamic, and interplay in highly dynamic yet organized interactions capable of orchestrating complex cellular functions
awkward phrasing. Perhaps it would be better to clearly make the point that organelle interactions are dynamic and studying them with high spatiotemporal resolution is important to understand their function in the cell.
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but either damaging the fragile living systems or poisoning the cellular health and both altering morphological and functional interpretations that follow.
perhaps "but this practice can increase phototoxicity to the live specimens and disrupt the normal morphology" would be more clear
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Thirdly, data-hungry nature ensued
awkard phrasing
-
enables tens of times photon budget increments
computationally enables a tenfold increase in the photon budget
-
holding a safe head
awkward phrasing
-
manifolds
"multifold"
-
differentiated ergo between
Not sure that "ergo" adds much meaning here. If it is wanted here then the punctuation should be, "differentiated; ergo, between"
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videography
Is it really videography? Is there a more precise term that can be used here?
-
much finer temporal scal
any quantitative estimate on the improvement from previous methods?
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50 times fluorescent dye concentratio
the concentration of fluorescent dyes 50-fold
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0.53 μm/s and 0.46 μm/s,
assuming these are average rates, is there a +/- standard deviation that can be reported?
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14.6 μW (0.5% of 488 nm)
Very impressive with such gentle excitation
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Rather scattered tissues of C. elegans exuberate the noise contaminations
Can this be clarified?
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We applied DeepSeMi to circumvent the problem, which enabled dual-color and high-SNR imaging at the 45.3 μW dosage at 488 nm and the 49.8 μW dosage at 561 nm over 30 minutes without apparent photodamage
Great use of specific language here.
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helps better observation of structures and functions of cells and organisms in vivo
is this implying that because of their transparency, there is decreased background/noise? Perhaps this should be clarified.
-
A very interesting computer-learning technique to improve signal to noise and enhance resolution of sub-cellular structures. The impact of this work will be more directly transmitted with clearer writing. Some specific suggestions are annotated throughout the paper.
One tool that might facilitate this is: https://hemingwayapp.com/
-
100 ×
100x
-
high-frame-rate
revise use of hypens throughout. three hyphens should not be used consecutively.
-
DeepSeMi
Use of DeepSeMi
-
50 times fluorescent dye concentratio
the concentration of fluorescent dyes 50-fold
-
in nonlinear microscope
using nonlinear microscopy or with a nonlinear microscope (and then specify which type)
-
helps better observation of structures and functions of cells and organisms in vivo
is this implying that because of their transparency, there is decreased background/noise? Perhaps this should be clarified.
-
Rather scattered tissues of C. elegans exuberate the noise contaminations
Can this be clarified?
-
holding a safe head
awkward phrasing
-
Fig. 4
Excellent figure to demonstrate the improvement in resolution with DeepSeMi over the raw images.
-
We applied DeepSeMi to circumvent the problem, which enabled dual-color and high-SNR imaging at the 45.3 μW dosage at 488 nm and the 49.8 μW dosage at 561 nm over 30 minutes without apparent photodamage
Great use of specific language here.
-
14.6 μW (0.5% of 488 nm)
Very impressive with such gentle excitation
-
vehemently enlarged
"drastically improved" would be better
-
much finer temporal scal
any quantitative estimate on the improvement from previous methods?
-
0.53 μm/s and 0.46 μm/s,
assuming these are average rates, is there a +/- standard deviation that can be reported?
-
brittle
what does brittle mean here?
-
fluctuated
what does fluctuated mean here?
-
Excitation power was set at 2% t
for which laser?
-
colors
suggest saying "fluorophores in different channels. They were: tagBFP-SKL (Ex/Em 402/457 nm),..." to give the excitation and emission spectra for each fluorophore.
-
commercial
what kind?
-
enables tens of times photon budget increments
computationally enables a tenfold increase in the photon budget
-
dye concentration
which dye concentration was better?
-
no-compromise results
can no-compromise results be defined clearly?
-
enlarged
increased is a better word choice than enlarged. Enlarged means to make bigger in size not magnitude. Increased is more accurate when talking about a larger number.
-
ten folds
tenfold
-
Besides,
Eliminate this.
-
differentiated ergo between
Not sure that "ergo" adds much meaning here. If it is wanted here then the punctuation should be, "differentiated; ergo, between"
-
videography
Is it really videography? Is there a more precise term that can be used here?
-
roots in
odd phrasing here. What is more direct verb that can be used here?
-
generality
generalizability might be better here
-
36,000 shots in multicolor
not a standard way to report this.
-
confocal microscope,
may want to specify the type of confocal here in addition to the methods.
-
Compared to recently developed interpolation-based denoising methods, DeepSeMi is capable of observing organelles of sophisticated movements and transformations without motion artifacts
Great point, may be stronger if framed as, "DeepSeMi improves upon interpolation-based denoising methods by (fill in the blank to describe what it is based on), which allows for observation of organelle dynamics without motion artifacts"
-
brand-
can eliminate to reduce redundancy
-
lustrous and remarkable advances in enriched fluorescence microscope[1, 9–12] have brought flourishing discoveries
awkward phrasing. Not sure what "enriched fluorescence microscope" really means
-
manifolds
"multifold"
-
clean data
more precise to say "data with high SNR"?
-
Thirdly, data-hungry nature ensued
awkard phrasing
-
but either damaging the fragile living systems or poisoning the cellular health and both altering morphological and functional interpretations that follow.
perhaps "but this practice can increase phototoxicity to the live specimens and disrupt the normal morphology" would be more clear
-
enlarging excitation dosage
"increasing laser power" ?
-
the contamination inevitable
specify the type of contamination
-
to be
should be "from being"
-
Such gorgeous patterns reflect live organelles of complex, dynamic, and interplay in highly dynamic yet organized interactions capable of orchestrating complex cellular functions
awkward phrasing. Perhaps it would be better to clearly make the point that organelle interactions are dynamic and studying them with high spatiotemporal resolution is important to understand their function in the cell.
-
magnificence of the harmonically orchestrated systems, organs, tissues, and cells
awkward phrasing. Perhaps something like "magnificently well-orchestrated systems of organs, tissues, and cells" or
-
and bio-friendly breaking the shot-noise limit, facilitating automated analysis of massive data about cell migrations and organelle interactions.
simplify and make more direct
-
The computationally 15-fold multiplied photon budget in a standard confocal microscope by DeepSeMi allows for recording organelle interactions in four colors and high-frame-rate across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames, all faithfully and sample-friendly.
consider making this a simpler, declarative statement(s)
-
all faithfully
awkward phrasing
-
requiring no clean data as references and no compromise of spatiotemporal resolution on diverse imaging systems
without the need for baseline data or loss of spatiotemporal resolution
-
efficacious
perhaps "effective" is more direct
-
bonds
should this be "bounds"?
-
