- Last 7 days
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Assigning individual nuclei to their respective cells is a non-trivial and often ignored issue in cell segmentation.
Fully agree! Would it be possible to add references to alternative approaches? I am also curious if you considered revising the segmentation based on unmatched nuclei. One could argue that the isolated nucleus in Fig. 2 should be re-labeled as not a nucleus.
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we resize images to 0.5 microns per pixel, as required by the models
As required by both models? Would it be possible to comment briefly on to what extent InstanSeg is scale-invariant?
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randomly assigning primary and secondary colours to each of the input channels
Is the RGB projection truly random or are the colors evenly spaced?
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During training, we only compute and backpropagate the loss using whichever labels are present in the ground truth. This method allows for the simultaneous prediction of nucleus and cell labels even when paired labels are not present in the ground truth.
Is the ground truth training data balanced between nucleus and cell labels or is this not necessary?
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- Sep 2024
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www.biorxiv.org www.biorxiv.org
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All supplemental materials are also included in the figshare link.
I'm curious if your light microscopy data used for cell tracking is, or could also be, made available?
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the recorded video was analyzed with ImageJ’s plugin TrackMate (6.01)
Cool video! I'm curious though if any filtering of the trajectories was done to prevent individual cells from being counted multiple times in the statistics? Relatively faster cells that dip in and out of focus, for instance, could skew the speed distribution if not taken into consideration.
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www.biorxiv.org www.biorxiv.org
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only one tile can be matched at a time
Sorry, but this also confuses me. How can this be considered a global transformation when only one tile is matched at a time for translation? I would have assumed that the tiles are roughly in place from using e.g. stage coordinates as a crude estimate of tile position.
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Although the algorithm can be used to only find the scaling and rotation parameters, the use of additional parameters will result in a clearer cluster, as the incorrectly matched pairs will be distributed over more dimensions. Therefore, it is beneficial to also add translation
Why do you say the algorithm can be used to "only find the scaling and rotation parameters" when you immediately add translation? Do you mean only scaling and rotation are solved for in the original implementation of the algorithm and your adaptation adds translation?
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When examining the transformation parameters that belong to pairs of resembling quadruplets, the correctly matched quadruplet pairs will cluster, as they all have similar transformations; on the other hand, the incorrectly matched pairs will be spread randomly across a larger space.
Your geometric hashing approach sounds similar to RANSAC. I am curious if you compared the two and what the tradeoffs between time and accuracy look like?
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since the imaging parameters of the sequencer were unknown
Hello, I am not very familiar with this imaging modality but it seems rather strange that the imaging parameters are unknown. Is this typically the case?
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- Aug 2024
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www.biorxiv.org www.biorxiv.org
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fields of view surpassing 50 cm2
This is indeed an impressive field of view, and the apparent SNR is impressive for ~10s exposures. More details on the laser power, diffuser, and detection optics would be appreciated!
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Pixel intensity profile along a line crossing the xiphoid cartilage on the mouse chest
Could you annotate the reference line in the plot to make it more clear where the pixel intensities in (c) are extracted from.
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we acquired SWIR Raman images from intact mice illuminated from 785 nm, a commonly used wavelength in Raman imaging, to 1064 nm, a red-shifted wavelength that extends Raman scattering wavelengths beyond the limits of standard InGaAs-based detectors
Could you provide information on the laser you used for this? It would be great if you could provide a more complete description of your experimental setup in a Methods section.
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the only necessary image processing being dark current correction
It's surprising to me that dark current poses more of a problem than autofluorescence. I'm curious if the dark current is somehow exacerbated when detecting in the SWIR region or if it would be mitigated simply with better detector cooling?
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- Jun 2024
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www.biorxiv.org www.biorxiv.org
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virtually stained images are intrinsically denoised because the models cannot learn to predict random noise.
Intrinsically denoised, sure, but noisy training data may still lead to a smoothed/blurred prediction. Are there techniques you have experimented with to sharpen predictions or has this not been an issue in your experience?
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Virtually and experimentally stained nuclei and membranes are segmented using the same Cellpose model.
For many applications the virtual staining could be seen as a means to an end: segmentation. Is the intermediate step of predicting the virtual stain necessary or would it be feasible to skip straight to the segmentation by e.g. merging the Cellpose segmentation model?
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trade-offs between spatial resolution, temporal resolution, number of channels, and photodamage
not to mention dataset sizes.
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- Mar 2024
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www.biorxiv.org www.biorxiv.org
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The predicted classes agreed well with the class representations and the fluorescence images themselves
Can this claim be quantified without deferring to a figure?
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Figure 1
The class representations of cell type 1 and cell type K are not very well differentiated.
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Supplementary Figures 1-2
IMO Supplemental figures 1 and 2 would be more clear and succinct as heatmaps than line plots.
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ideal
You provide a clear explanation of how you generate the pseudospectra in the methods, but I question the use of "ideal" in describing them. I get that you mean idealized, but it sounds as if they are perfect and in no way subjective which is misleading.
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In a test set of 50 image tiles per dataset
Could you please clarify if this test was done by using manual segmentation as ground truth? If not, what was the source of ground truth data used to compute F1-scores?
An F1-score of 0.7 is not generally seen as very high. Could emphasize more strongly in your discussion the power of your approach (combining the instance segmentation with class maps for classification) given that this seems to be a non-trivial segmentation problem.
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- Feb 2024
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www.biorxiv.org www.biorxiv.org
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The extended exposure time can also achieve an even better SNR than that in coherent Raman microscopy [1].
Is this claim quantitatively verified?
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Exposure times were 5 s/line and 30 s/line for imaging the live and cryofixed samples, respectively.
How is this a fair comparison for comparing SNR between live and cryofixed conditions? I understand your point that exposure time for live Raman is limited due to photodamage, but would still be interesting to see 30s/line for live Raman (albeit with drift artifacts) for the sake of comparison.
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exposure with compensating
*exposure, compensating
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We confirmed the band width of 3.9 cm-1 at 1001 cm-1, assigned as phenylalanine, in the cryofixed conditions, whereas the same peak was observed to be 8.6 cm-1 under a practical Raman measurement condition at room temperature (Fig. 1F).
This is a nice example of benchmarks for band widths for certain spectral peaks to differentiate between low and high SNR!
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high-SNR Raman imaging
Can you more clearly define what constitutes "high-SNR" Raman? Of course it is high relative to "low-SNR" Raman, but how can someone know if they are doing high- vs low-SNR Raman? Are there thresholds that are (or can be) defined on the width of certain spectral peaks?
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fused silica coverslip
Is fused silica necessary to prevent autofluorescence from surface defects in normal glass coverslips? Is it typical/recommended to used fused silica for Raman microscopy generally or only for very high sensitivity measurements?
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shows
*show
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wavelengthdispersion
*wavelength dispersion
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Additionally, the utility of the chemical fixation is limited in fixing biological activities in motion [24], and there are molecular species that cannot be fixed by the current chemical fixation techniques [25].
Would be helpful to cite a couple specific examples of biological activities and/or molecular species for which fixation is insufficient to bolster motivation for cryogenic freezing.
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