There are various ways to get images out of Cytobank. Click the links to jump to the sections below.
Images in Cytobank 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, .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 image exported at different resolutions, but shown at the same size. Low resolution images cannot scale to a large size)
Plot size / resolution can be adjusted easily in the control panel on the left side of the Working Illustration:
(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 Cytobank, SPADE trees, the Sunburst, and the Population Tree can be exported as SVG. Other images such as dot plots, histograms, contour plots, and heatmaps cannot (see SVG Plots Section below for a slight exception to this), although heatmaps do scale well regardless because of their simplicity.
Exporting compatible images from Cytobank 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.
A common request is to be able to export typical plot types (e.g. dot, contour, histogram) as SVG. This isn't possible in Cytobank because plots are currently limited to bitmap format. In order to support workflows related to SVG in the meantime, however, functionality is available to create plots that use SVG for fonts and labels, but with normal bitmap images embedded for the data visualization. The effect is that data plots themselves will look the same, but their labels will appear in crisp vector format ready for presentation, publication, or further modification to styling and layout in a vector image editing software such as Adobe Illustrator or free alternatives such as Inkscape. See instructions below for exporting complete illustrations as SVG or individual plots as SVG.
Cytobank supports the export of complete illustrations as SVG vector format with layout conserved. As discussed above, when exported, the plots within the illustration will be bitmap images embedded with labels and layout that are otherwise 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)
The button to export an entire illustration as SVG can be found within the Working Illustration in the page-level navigation bar:
(button location to export an entire illustration as SVG)
Currently the functionality to export entire figures as SVG is limited to Mozilla Firefox browser. The entire illustration must be fully loaded before the export can happen. Heatmap plot type cannot currently be exported. Note that large illustrations may take longer to export. Note that the SVG Plot toggle (see below) does not need to be enabled to export the illustration as SVG. The functionalities are independent.
Besides exporting illustrations as SVG, Cytobank also supports the rendering of SVG plots within the Working Illustration. This functionality is independent from the export functionality and does not need to be enabled to export illustrations as SVG (see above).
In the control panel of the Working Illustration there is a toggle for turning SVG Plots on and off:
When the SVG Plots toggle is turned on, plots in the illustration will appear as SVG format instead of the typical PNG format. The effect can be seen when taking screenshots that are zoomed in:
(zoomed in screenshots taken with default mode on left and SVG Plots enabled on right. The labels do not suffer from loss of clarity upon zooming for the SVG plot)
For most cases, having SVG Plots enabled won't have a practical benefit for simply perusing data in the Working Illustration. However, if a small number of plots are needed in SVG format it can be simpler to load them in the illustration then save them individually as SVG files by right-clicking and saving. Alternatively, if screenshots are being taken it can provide better label clarity as demonstrated in the image above.
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 Cytobank or you have no need to give them access to the experiment. Screenshots are also good for grabbing groups of plots from an illustration when drag and drop is not ideal.
If you have a PC: If your version of Windows does not have the snipping tool, search around on the web for the many free alternatives.
If you have a Mac: Apple computers have a simple and fast native screenshot tool.
Note, heatmaps are only draggable from the Print View of the illustration. Other plot types are draggable at any time. (may not work for all combinations of browser, operating system, and software).
(example of drag and drop to PowerPoint)
After right clicking on an image you will have the option to copy or save it. After copying, the image can be pasted elsewhere. (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 printer-friendly version of any Cytobank Illustration, click the print view button. If you have issues with illustration formatting with the normal print view, use the formatting conserved feature (see section below).
(open a printer-friendly view of the Working Illustration)
Any illustration can be exported as PDF by clicking the PDF button from the Working Illustration. After clicking this button, you will have the option to choose a size of the PDF. The PDF that is exported will look like the printer-friendly view of the illustration, but will also be affected by the size the PDF that you choose to export. The "infinite" resolution option is generally the best choice for conserving formatting from Cytobank to the PDF. If you experience formatting issues with the infinite option, see the section below on conserving formatting.
Occasionally there are formatting issues with the normal print view and PDF of an illustration. This typically manifests as layouts being stacked vertically instead of extending horizontally. There are various ways to get a PDF of an illustration without formatting and layout issues:
Via SVG intermediate
Export the complete illustration as SVG. Afterwards, open the SVG with a web browser and follow the directions below for creating a PDF via browser controls. Alternatively, open the SVG with a software that supports the format and export as PDF.
Via "simple print view"
A beta feature called "simple print view" exists in Cytobank to format illustrations accurately for conversion to PDF. To use it, setup the Working Illustration as desired and then append "/simple_print_view" to the current URL and click "enter" or "return" on your keyboard. An example URL will end up like this: https://yoursitename.cytobank.org/cytobank/experiments/###/illustration/###/simple_print_view
When the simple print view is created, follow the directions below to export the PDF through the browser.
Creating a PDF via browser controls
Exporting a PDF of this simple print view is not as simple as clicking a button in the Cytobank interface, but instead requires a bit of extra effort to create a PDF via your browser's native tools.
In your web browser, choose the print option (normally within the file menu). From the print dialog, look for an option to divert the print job to a PDF. This functionality and the options that come with it vary by browser. To take whatever PDF your browser thinks is best, choose the most obvious options for export, which should be clear in the print dialog.
If you are dissatisfied with the layout of the exported PDF, some browsers allow tailoring the dimensions of the exported PDF. On Chrome for Mac the exact size of the PDF can be chosen to avoid page breaks or truncations. The commands are as follows: File Menu -> Print -> Print using system dialog -> Paper size -> Manage custom sizes. Then specify the dimensions that result in a satisfactory PDF and click to export. It may take multiple attempts to get the desired size.
As mentioned above, the Population Tree, Sunburst, and SPADE trees can be exported as SVG for any of their attributes to be manipulated in an external software. Other plot types such as histogram, dot plot, contour plot, etc., should be exported as SVG for simple manipulation of labels. Heatmaps do support a modified copy-paste workflow for easy font editing (see animation above).