ITQB Preprint Journal Club: 21 September 2018
and 1 collaborator
UIUC Plant Physiology Journal Club: 2018-09-05
- The authors state “many researchers are likely to manually count stomata” - is this because other methods are not good enough, user interface is too complicated or just people liking more traditional things?
- In the methods it is written “final fully connected layers by convolutions”. Does this mean there's no fully-connected layers, only convolutional layers? It sounds like both are included in other parts of the paper.
- We were confused by the statement “we argue that the current architecture does not transfer well to different scales and images should be pre-processed to match the training scale of the network,” is that not the reason a fully-convolutional network is used? to avoid the inability to manage different input sizes.
- Consider making legends of Figure 3 and Figure 4 bigger to improve readability
- Figure 5 is very informative and summarizes the data well
- Figure 6 might be improved by including an inset to focus on the down number.
- Figure 7 - scale bars
- There was a strong linear correlation at higher magnification between DCNN and human counts is this a standard magnification for this type of experiment?
- It would be good to include:
- Quantification of the accuracy of the automatic separation between abaxial and adaxial datasets. A failure of separation could potentially have contributed to finding stomata on the "adaxial" cuticle.
- Discussion of whether the magnifications (200x and 400x) are suitable for this kind of analysis.
- Information about why the 4 sources of images were chosen and discussion of whether they provide enough of a range.
- An explanation of why data was which showed <98% was discarded
- Stats on Gingko and poplar datasets.
- Might consider rephrasing “the mean number of stomata detected in the adaxial, aorta, and breast cancer image sets was 1.5, 1.4, and 2.4, respectively, while the mean value of the abaxial set was 24.1” to better explain the low frequency: to compare with non-stomata dataset vs dataset that has very low number of stomata
- Code availability: It would be helpful if the code and custom scripts (such as separation of abaxial and adaxial leaf sides) are made available and linked to a repository.
UIUC Plant Physiology Journal Club: 2018-08-13
PREreview of bioRxiv article “Convergent evolution of effector protease recognition by Arabidopsis and barley”
LaNeC Journal Club - PREreview of ?
and 2 collaborators
LaNeC Journal Club - PREreview of "Differential encoding of predator fear in the ventromedial hypothalamus and periaqueductal grey"
and 1 collaborator
PREreview of "Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation"
Journal Club EcoEvol #02 - 06.07.2018
and 2 collaborators
UIUC preprint journal club : 2018-07-30
- Keywords: Consider revisiting, as many of the keywords are already on the title. Additionally, it would be helpful to include terms rather than acronyms which are not familiar to non-experts.
- Introduction: Would be good to include examples of some of the limitations to automated confocal microscopy approaches to orientate readers.
- Line 143: (Atwell et al., 2010). This citation doesn't seem to be right. If the author is referring to genomic heritability it could cite de los Campos et al. (2015).
- Methods: Would like to see further information on the methodology used for carbon isotope discrimination in the main text
- Results: Might consider using the term ‘genetic-heritability’ rather than ‘pseudo-heritability’
- Results: Direct comparison with previously reported dC13 values for accessions that have been demonstrated to differing WUE would be helpful.
- Figure 4: the text on the figure is likely to be too small to see properly
- Line 505: “soil composition...” This is a really interesting point about the complexity of environmental effects on plant physiology. It might be helpful to provide some explanation for readers less familiar with soil content. (e.g. water holding content and effect on root structure - e.g.https://doi.org/10.1073/pnas.1721749115)
- Line 499-500. Repetition of text on 498-499
- Results: It would be helpful to share where the functional annotation for genes come from. This gene appears to be involved in mRNA decapping. There is only one publication, which found it is involved in PAMP triggered immunity, plants were dwarf in stature. TAIR does not annotate a role in cell differentiation (10.15252/embj.201488645)
- Discussion: It is interesting to see a comparison with a related species and how the observed pattern is consistent between the two.
- Data accessibility: This is excellent. Great to see that all data and code will be made available and deposited in a permanent repository!