Understanding the structure–function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.

/pdf/microscopy-image-browser-a-platform-for-segmentation-and-13c1m9oldc.pdf

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets.

Toothguide Trainer tests with color vision deficiency simulation monitor

The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

Inward rectifying potassium channels (Kir) are a large family of ion channels that play key roles in ion homeostasis in oligodendrocytes, the myelinating cells of the central nervous system (CNS). Prominent expression of Kir4.1 has been indicated in oligodendrocytes, but the extent of expression of other Kir subtypes is unclear. Here, we used qRT-PCR to determine expression of Kir channel transcripts in the mouse optic nerve, a white matter tract comprising myelinated axons and the glia that support them. A novel finding was the high relative expression of Kir7.1, comparable to that of Kir4.1, the main glial Kir channel. Significantly, Kir7.1 immunofluorescence labelling in optic nerve sections and in isolated cells was localised to oligodendrocyte somata. Kir7.1 are known as a K+ transporting channels and, using patch clamp electrophysiology and the Kir7.1 blocker VU590, we demonstrated Kir7.1 channels carry a significant proportion of the whole cell potassium conductance in oligodendrocytes isolated from mouse optic nerves. Notably, oligodendrocytes are highly susceptible to ischemia/hypoxia and this is due at least in part to disruption of ion homeostasis. A key finding of this study is that blockade of Kir7.1 with VU590 compromised oligodendrocyte cell integrity and compounds oligodendroglial loss in ischemia/hypoxia in the oxygen-glucose deprivation (OGD) model in isolated intact optic nerves. These data reveal Kir7.1 channels are molecularly and functionally expressed in oligodendrocytes and play an important role in determining oligodendrocyte survival and myelin integrity.

/pdf/a-critical-role-for-the-inward-rectifying-potassium-channel-1yaq7twpcr.pdf

A critical role for the inward rectifying potassium channel Kir7.1 in oligodendrocytes of the mouse optic nerve.

High-throughput analyses of single-cell microscopy data is a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a software package that allows researchers to transform cell segmentation and spot detection data generated by different programs automatically into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP runs in R, which enables the use of advanced statistical analysis tools as well as easily adjustable plot graphics in every operating system. Using BactMAP we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap.

https://www.biorxiv.org/content/biorxiv/early/2019/08/07/728782.full.pdf

BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data

The objective of this project is to establish a practical application of the concept of Color Universal Design (CUD), the
design that is recognizable to all color vision types.
In our research, we looked for a clearly distinguishable combination of hues of four colors - black, red, green, and blue -
which are frequently used in these circumstances. Red-green confusion people do not confuse all kinds of red and all
kinds of green. By selecting particular hues for each color, the ability to distinguish between the four colors should be
greatly improved.
Our study thus concluded that, by carefully selecting hues within the range of each color category, it is possible to
establish color-combinations which are easily distinguishable to people of all color-vision types in order to facilitate
visual communication.

/pdf/color-universal-design-the-selection-of-four-easily-1dk6qff9rq.pdf

Color universal design: the selection of four easily distinguishable colors for all color vision types

This report is af ollow-up to SPIE-IS+T / Vol 7528 7528051-8, SPIE-IS+T / Vol 7866 78660J-1-8 and SPIE-IS+T / Vol 8292 829206-1-8
Colors are used to communicate information in various situations, not just for design and apparel However, visual information given only by color may be perceived differently by individuals with different color vision types Human color vision is non-uniform and the variation in most cases is genetically linked to L-cones and M-cones Therefore, color appearance is not the same for all color vision types Color Universal Design is an easy-to-understand system that was created to convey color-coded information accurately to most people, taking color vision types into consideration In the present research, we studied trichromat (C-type), prolan (P-type), and deutan (D-type) forms of color vision
We here report the result of two experiments The first was the validation of the confusion colors using the color chart on CIELAB uniform color space We made an experimental color chart (total of color cells is 622, the color difference between color cells is 25) for fhis experiment, and subjects have P-type or D-type color vision From the data we were able to determine "the limits with high probability of confusion" and "the limits with possible confusion"
around various basing points The direction of the former matched with the theoretical confusion locus, but the range did not extend across the entire a* range The latter formed a belt-like zone above and below the theoretical confusion locus This way we re-analyzed a part of the theoretical confusion locus suggested by Pitt-Judd The second was an experiment in color classification of the subjects with C-type, P-type, or D-type color vision The color caps of fhe 100 Hue Test were classified into seven categories for each color vision type The common and different points of color sensation were compared for each color vision type, and we were able to find a group of color caps fhat people with C-, P-, and D-types could all recognize as distinguishable color categories The result could be used as the basis of a color scheme for future
Color Universal Design

Color universal design: analysis of color category dependency on color vision type (2)

Color universal design: analysis of color category dependency on color vision type (3)

Our projects are founded on the principles of Color Universal Design (CUD), the objective of which is to promote public information systems, such as train maps, which feature colors recognizable to all color vision types 1) . In this paper, we were looking for a red which would be clearly distinguishable protan-vision people who see some tone of red as a dark color and consequently confuse it with black. These potentially kinds of red were represented on the Yokohama City Subway map, which we were presented with. We at the CUD believe it is possible to establish color design which is easily distinguishable to people of all color-vision types in order to facilitate excellent visual communication.

Color Universal Design The Optimal Representation of the Color Red for Protan-Vision People: Practical Alternatives from the Color Universal Design Organization

Kei Ito

Papers

Color universal design: the selection of four easily distinguishable colors for all color vision types

Color universal design: analysis of color category dependency on color vision type (2)

Color universal design: analysis of color category dependency on color vision type (3)

Color Universal Design The Optimal Representation of the Color Red for Protan-Vision People: Practical Alternatives from the Color Universal Design Organization