Watch our introduction to viSNE video of viSNE being run and analyzed on a public example dataset.
For more reading, visit the table of contents for articles on viSNE.
What is viSNE?
How do I analyze my viSNE results or export data?
Since viSNE results are two added channels within an FCS file, all the same tools to analyze FCS data can be used to analyze viSNE results. See our article on analyzing and interpreting viSNE results for some ideas.
Where is my viSNE analysis?
The viSNE analysis can be found on the Experiment Summary page of the original Cytobank Experiment alongside SPADE or CITRUS analyses under the “Advanced Analyses” section. It is also possible to access a viSNE analysis via the dropdown viSNE shortcut menu at the top of the experiment page. A viSNE analysis can be cloned and it will show up in the Experiment Manager as a cloned experiment.
Does viSNE downsample or upsample data?
Unlike SPADE, viSNE does not do any downsampling or upsampling of the data selected for analysis. The data selected for viSNE analysis during setup are used in their entirety throughout the analysis. The only downsampling that may occur is a result of having more events in the source files than are selected for viSNE. In this case, the original files are randomly downsampled based on proportional or equal event sampling as specified when setting up the viSNE analysis
I am not allowed to run viSNE, why?
viSNE is a premium functionality and only available on Premium and Enterprise Cytobank.
Creation of a new viSNE analysis is only accessible by users with Illustration level project access or higher to an Experiment. You may not have sufficient access to the Cytobank Experiment in question.
What does the distance between two points on a viSNE plot mean?
If events are grouped together on the viSNE map, they are similar to each other based on all the channels included in the run. However, the distance between points on a viSNE map isn’t proportionally related to how dissimilar they are. For this reason, you shouldn’t use viSNE map coordinates (the tSNE1 and tSNE2 channels) as input into algorithms or models that assess their association with other variables.
Can I run viSNE on fluorescent data?
viSNE can be run on FCS data regardless of instrument origin. With fluorescent data sets, however, proper compensation is important, and more attention may need to be paid to proper scale settings.
Which FCS files should I select for my viSNE analysis and what files are generated?
The FCS files to select for viSNE analysis depend on what is being examined in the experiment. viSNE combines all data selected for analysis and creates a new FCS file for each population-file combination. Each new file has new tSNE channels which can then be visualized in Cytobank as channels.
Why do my viSNE plots look slightly different when run on the same data set?
Although viSNE plots tend to have similar groupings of cell subsets, viSNE plots may look slightly different because the algorithm is stochastic. Additionally, because t-SNE uses a non-convex objective function, different runs may occasionally give very different solutions. It’s okay to run viSNE multiple times and pick the one that gives the best visualization. If you’re interested in re-running viSNE on the same data with the same settings and getting the exact same map (e.g. for validation of a workflow), you can set the seed.
Why is there a (v) in the channel names in viSNE experiment?
A (v) appears in the channel name of viSNE files to indicate the channels that were used in the creation of the viSNE map. The channel name can be edited on the channel annotation page by clicking “setup” on the channels figure dimension in the working illustration.
Can I run viSNE or SPADE on my viSNE-generated FCS files?
Yes. To do this, click to start a new viSNE or SPADE run from the viSNE experiment. Cytobank will clone the viSNE analysis and create a cloned experiment accessible from the Experiment Manager. SPADE or viSNE can then be executed from within this cloned experiment. It is not advised to run viSNE on the tSNE channels of an existing viSNE analysis because this yields poor results, even though one might try to do this to clean up an existing viSNE map.
Why is the symbol for viSNE a cherry?
If you Google "viSNE" and look at the image results, it should be clear. A deeper explanation of why this is the case will be left as an exercise to the reader.