How to Use Color Blind Friendly Palettes to Make Your Charts Accessible
August 1, 2023 | Figure & Color
使用场景
高水平SCI论文的发表要求所有的图均是红绿色盲人员友好的。详细解释见：Colour me better: fixing figures for colour blindness
解决办法
推荐以下方法选取正确的颜色。
网页工具
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i want hue : 可根据所需颜色数量选取需要的红绿色盲可见的颜色类型。
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Chroma.js Color Palette Helper
R 包
There are lots of packages already collected lots of safe colors. I list some of them, but not limited here.
library(RColorBrewer)
display.brewer.all(colorblindFriendly = T)
remotes::install_github("wilkelab/cowplot")
install.packages("colorspace", repos = "http://R-Forge.R-project.org")
library(ggplot2)
ggplot(iris, aes(Sepal.Length, fill = Species)) +
geom_density(alpha = 0.7) + scale_fill_OkabeIto()
如何处理显微镜图片用于文章发表
August 1, 2023 | Figure
Cheat sheets for Image publishing
Images, initially drawings now photos, are widely used in biology and medicine but when published not always understandable.
Image Workflow for Novice Users
When preparing images for publication, the sequence and proper use of software matters to truthfully report observations. During the first lock down, Christopher Schmied and I therefore created cheat sheets that explain a most basic workflow to get everyone from microscope data to figure in a few simple steps.
Cheat Sheets
The workflow is summarized in two printable cheat sheets. One cheat sheet explains the steps towards a publishable image, the second cheat sheet how to implement the steps with ImageJ/FIJI image processing software.
Download
Get the cheat sheets as printable PDF, high-res pdf and psd.
Note, we used an open license, that means you can get the adaptable files and e.g., make translations, alterations, or add your own notes.
A German version was already made by Joram Schwartzmann, checkt it out!
Further resources
Beyond our starter cheat sheets more great resources help you along the way: The “Biologist’s guide to planning and performing quantitative bioimaging experiments” describes the entire arc from sample to microscope via image analysis towards data interpretation and publication. The resource lists many key points and aggregates links to more detailed descriptions, making it easy for biologists to navigate their first microscopy experiments.
More about
Microscopy image acquisition
- Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. North, A.J., 2006. J Cell Biol
- Fluorescence microscopy–avoiding the pitfalls. JBrown, C.M., 2007. Cell Sci 120, 1703–1705.
- Rigor and Reproducibility in Confocal Fluorescence Microscopy. Jonkman, J., 2020. Cytometry A
Fluorophores and Filters
- Optimizing live-cell fluorescence imaging conditions to minimize phototoxicity. Kiepas, A., Voorand, E., Mubaid, F., Siegel, P.M., Brown, C.M., 2020. J Cell Sci.
- Assessing phototoxicity in live fluorescence imaging.Laissue, P.P., Alghamdi, R.A., Tomancak, P., Reynaud, E.G., Shroff, H., 2017. Nat Methods
- Recommendations for a standardized nomenclature for probe tags used in cytometry and microscopy imagingBlenman, K.R.M., Spidlen, J., Parks, D.R., Moore, W., Treister, A., Leif, R., Bray, C., Goldberg, M., ISAC Data Standards Task Force, Brinkman, R., 2021. ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging. Cytometry A
Sample preparation
- Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. North, A.J., 2006. J Cell Biol
Method reporting
- Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.Hammer, M., Huisman, M., Rigano, A., Boehm, U., Chambers, J.J., Gaudreault, N., North, A.J., Pimentel, J.A., Sudar, D., Bajcsy, P., Brown, C.M., Corbett, A.D., Faklaris, O., Lacoste, J., Laude, A., Nelson, G., Nitschke, R., Farzam, F., Smith, C.S., Grunwald, D., Strambio-De-Castillia, C., 2021. Nat Methods
- A guide to accurate reporting in digital image acquisition - can anyone replicate your microscopy data?Heddleston, J.M., Aaron, J.S., Khuon, S., Chew, T.-L., 2021. J Cell Sci
- Best practices and tools for reporting reproducible fluorescence microscopy methods. Montero Llopis, P., Senft, R.A., Ross-Elliott, T.J., Stephansky, R., Keeley, D.P., Koshar, P., Marqués, G., Gao, Y.-S., Carlson, B.R., Pengo, T., Sanders, M.A., Cameron, L.A., Itano, M.S., 2021. Nat Methods
- Imaging methods are vastly underreported in biomedical research. Marques G, P.T., Sanders MA, 2020. Elife
- Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.Rigano, A. et al. Nat. Methods
- MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. Ryan, J., Pengo, T., Rigano, A., Llopis, P.M., Itano, M.S., Cameron, L.A., Marqués, G., Strambio-De-Castillia, C., Sanders, M.A., Brown, C.M., 2021. Nat Methods
Image analysis & processing software
- Fiji: an open-source platform for biological-image analysis.Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Nature methods
- A Hitchhiker’s guide through the bio-image analysis software universe.Haase, R., Fazeli, E., Legland, D., Doube, M., Culley, S., Belevich, I., Jokitalo, E., Schorb, M., Klemm, A., Tischer, C., 2022. FEBS Lett
- Reproducible image handling and analysis. Miura K NS. EMBO J. 2021;40(3):e105889.
Cotton Single Cell Assembly and Gene Annotation
August 1, 2023 | Genome
About Adelphocoris suturalis
Assembly
Annotation
Statistics
References
More information
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