and identify damaged cells to exclude from downstream processing
What indicates cell damage from 488 nm autofluorescence?
253 Matching Annotations
- Feb 2023
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www.biorxiv.org www.biorxiv.org
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implementing culture independent methods to study planktonic cells in their native ecosystem is truly important to better understand the cellular biology of these ecologically relevant microorganisms
This is an excellent point and justification for this study.
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ogether with the 488nm excitation channel, an image of the transmitted laser light was generated using the T-PMT detector of the microscop
What was the autofluorescence excited by 488 nm indicating in the samples?
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- Dec 2022
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www.biorxiv.org www.biorxiv.org
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50 times fluorescent dye concentratio
the concentration of fluorescent dyes 50-fold
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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.
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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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holding a safe head
awkward phrasing
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14.6 μW (0.5% of 488 nm)
Very impressive with such gentle excitation
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much finer temporal scal
any quantitative estimate on the improvement from previous methods?
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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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Excitation power was set at 2% t
for which laser?
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enables tens of times photon budget increments
computationally enables a tenfold increase in the photon budget
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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?
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36,000 shots in multicolor
not a standard way to report this.
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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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Thirdly, data-hungry nature ensued
awkard phrasing
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manifolds
"multifold"
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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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enlarging excitation dosage
"increasing laser power" ?
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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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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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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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100 ×
100x
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high-frame-rate
revise use of hypens throughout. three hyphens should not be used consecutively.
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DeepSeMi
Use of DeepSeMi
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in nonlinear microscope
using nonlinear microscopy or with a nonlinear microscope (and then specify which type)
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Fig. 4
Excellent figure to demonstrate the improvement in resolution with DeepSeMi over the raw images.
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vehemently enlarged
"drastically improved" would be better
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brittle
what does brittle mean here?
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fluctuated
what does fluctuated mean here?
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commercial
what kind?
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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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dye concentration
which dye concentration was better?
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no-compromise results
can no-compromise results be defined clearly?
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ten folds
tenfold
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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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Besides,
Eliminate this.
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roots in
odd phrasing here. What is more direct verb that can be used here?
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generality
generalizability might be better here
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confocal microscope,
may want to specify the type of confocal here in addition to the methods.
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brand-
can eliminate to reduce redundancy
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clean data
more precise to say "data with high SNR"?
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the contamination inevitable
specify the type of contamination
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to be
should be "from being"
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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
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all faithfully
awkward phrasing
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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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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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efficacious
perhaps "effective" is more direct
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bonds
should this be "bounds"?
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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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