There are various ways to get images out of the Cytobank platform. Click the links to jump to the sections below.
- Bitmap images
- SVG graphics
- Complete Illustration Layout
- Individual plots
Images in the Cytobank platform can be broadly classified into two categories with regard to the way in which they store information and their ability to scale to different sizes:
1) Bitmap or Raster images are grids of pixels, where each pixel in the grid has a color. Common formats are .png, .jpg, or .gif. These images have limited ability to scale to a large size without compromising quality, as is apparent in the following example:
(two of the same plot images exported at different resolutions, but shown at the same size. Low resolution images cannot scale to a large size)
Plot size or plot resolution can be adjusted easily in the Plot tab of the Illustration Editor navigation bar:
(Adjust plot size / resolution)
2) Vector or SVG images don't store their underlying information with coordinates, but instead with relationships between image components that are represented mathematically and proportionally. Because the components of the image emerge from equations that describe their relationships relative to each other, and not from exact coordinates, vector images can scale infinitely without compromising quality.
In the Cytobank platform the Illustration Editor uses SVG for fonts and labels, but normal bitmap images embedded for the data visualization within the plots. As a result, data plots themselves will look the same independently of the type of file that you select to export and would only vary dependent on the plot size selected. If you select PNG as your exporting format, the entire illustration (plots, fonts and labels) would be a bitmap image. However, if you choose to export the illustrations as SVG the labels would appear in crisp vector format ready for presentation, publication, or further modification to styling and layout in a vector image editing software. See instructions below for exporting complete illustrations as SVG or individual plots as SVG.
Export Complete Illustration layouts
The Cytobank platform supports the export of complete illustrations as PNG, SVG or PDF files. As discussed above, when exported, the plots within the illustration will be bitmap image embedded. If PDF or SVG is chosen as export file, labels and layout will be vector-based. This allows for simple adjustments to label text and the layout of groups of plots created in an illustration.
(demonstration of changing label font size and layout of an exported illustration)
To export an entire illustration, click on the Export tab of the Illustration Editor navigation bar. A drop-down menu will appear with the following settings:
- Name of the file
- Type of file: select .pdf, .png or .svg
- Export options (see below)
Once you have selected the settings click on the Export button and the file will be automatically downloaded to your computer.
(Export tab and drop-down menu to export an entire illustration)
Export Individual plots
If you want to export just some individual plots, mouse over the plot and a window will automatically appear. Click on the Export button in the upper right corner of the window. A drop-down menu will appear with the SVG, PDF and PNG options. Select one and the file will automatically download to your computer. As discussed above, when exported, the plots will be bitmap images embedded with vector-based labels if SVG or PDF was selected. Note that Individual plot export is not available for heatmaps.
Taking a screenshot is often the fastest and easiest way to share an image for sending to a colleague if they do not have access to the Cytobank platform or you have no need to give them access to the experiment.
If you have a PC: If your version of Windows does not have the snipping tool, search on the web for the many free alternatives.
If you have a Mac: Apple computers have a simple and fast native screenshot tool.
After right clicking on an image you will have the option to copy or save it. After copying, the image can be pasted elsewhere (this may not work for all combinations of browser, operating system and software).
(any image can be right-clicked for a context menu from which it can be copied or saved)
For a print view of any Cytobank Illustration, click the Print view button. If you have issues with illustration formatting with the normal print view, use the Export tab of the Illustration Editor navigation bar discussed before.
Export SPADE trees, Sunburst and Population Tree as SVG
In the Cytobank platform, SPADE trees, the Sunburst, and the Population Tree can be exported as SVG. Exporting compatible images from the Cytobank platform as SVG requires a light-weight third-party tool called SVG Crowbar. It is available for free from the New York Times. You must use Google Chrome browser and follow the directions that appear on the linked page. After the button is available in your browser, view any SVG image and click the SVG Crowbar button to export the image as SVG. You will need a software package capable of viewing and editing SVG graphics (e.g. Adobe Illustrator or free alternatives such as Inkscape) to work with the file. With SVG, any aspect of the image can be individually accessed and modified, including fonts and colors.
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