Cytobank Frequent Asked Questions

 

Account Issues

  • How do I renew my Premium subscription to Cytobank?
  • What do I do if I got locked out of my account?
  • What to do with a Cytobank account if the owner leaves the organization?

Data Sharing

  • Can I remove the sharing once the data is shared with someone?
  • How can I share experiments between Cytobank servers?

Illustrations

  • How do I make overlaid viSNE maps to highlight a rare population?

FCS files

  • Are the FCS files generated from my cytometer compatible with Cytobank?
  • What is the difference between download files, export events, and split files by population?
  • Why did my FCS filename change when I exported events or split files by population?
  • How can I concatenate my FCS files?

Behind the scenes

  • When will my task be completed?
  • Why is my experiment “in queue”?

Account issues

  • How do I renew my Premium subscription to Cytobank?

-If you need a quote, please write in to sales@cytobank.org.
-If you pay by credit card, you can renew from within your Cytobank account. Click your username from the top-right corner of your browser to access your account settings.

  • What do I do if I got locked out of my account?    

For security purposes, Cytobank will automatically inactivate an account if unusual login activities been detected, such as high-frequency logins from different locations and devices. If you are locked out, please write in to support@cytobank.org

  • What to do with the Cytobank account if the account owner leaves the organization?

There are a few ways around it. You may choose to transfer that account to another person's name by change the first/last name and associated email address in the account profile. Please keep in mind that the associated username can't be changed nor altered in any way. Or as we may suggest is to organize the experiments in that account under projects and then add another person as the project manager. This way, the experiment manager will have full control of the data in that account even after the subscription expired.   

Data Sharing

  • Can I remove the sharing once the data is shared with someone?

Absolutely, you may remove sharing at any time. You can do so by click on the Sharing tab on the upper right corner and then cross out the person you wish to remove access to the data. 

  • How can I share experiments between Cytobank servers?

 - Designed for data security, different Cytobank servers are completely independent.                 Experiments can only be shared through the “Sharing” link with users on your own server. 

- See instructions here for transferring individual experiments through exporting an ACS file or accessing a collaborator’s server for ongoing collaboration.

 Illustrations

  • How do I make overlaid viSNE maps to highlight a rare population?

To make flashy viSNE overlays like the ones featured in Kordasti et. al., Blood, 2016 (fig. 2), follow these steps:  

  1.  In the working illustration, select the population on which you ran viSNE for your background plot.
  2. Activate these settings:
      • Plot Type = Contour or Dot
      • Color by = None (if Contour), Black (if Dot) or Density
      • Palette = Grayscale
  3. Right-click and copy your plot into your favorite image editor. 

image3.png

4. Return to working illustration and select the population you want to feature in the foreground. Plot Type and Color by choices are the same as above. Choose your favorite color palette (examples shown below). Right-click and copy your plot into the image editor.  

image2.png

    5. Make the background of the featured foreground plot transparent. (Query the editor’s help files if you need.)

Example in Microsoft PowerPoint ® for Mac: 

image1.png

6. Drag the featured plot on top of the background or align them with your image editor’s alignment controls

Untitled.png

FCS files

  • Are the FCS files generated from my cytometer compatible with Cytobank?
  1. Instrument acquisition software that does not adhere to FCS file standards during export can lead to compatibility issues with some algorithms in Cytobank, particularly with SPADE. Generally, if there are FCS keyword formatting issues that prevent SPADE runs, you can re-write the FCS files in Cytobank by exporting events
  2. The dynamic range of different instruments may require different optimal scale settings (min, max, transformation argument). For most common instruments, Cytobank will detect the instrument and apply a specific set of scales as default. However, you should always check your scales settings at the beginning of your analysis.
  3. Cytobank can read FCS 2.0, 3.0, and 3.1 files from any instrument. Some cytometer acquisition software may require special attention.
  4. Additionally, you can upload any type of tab-delimited data using DROP.
  • What is the difference between download files, export events, and split files by population?

          - There are many ways to export your FCS data depending on your needs. In summary:

export_table.png 

  • Why did my FCS filename change when I exported events or split files by population?

Sometimes you can end up with really long filenames resulting from exporting files based on populations in the Working Illustration. To help with tracking the providence of your data, the population name will be appended to the end of the filename. You can edit the filenames on your desktop after export if needed. 

  • How can I concatenate my FCS files?

See instructions for concatenating your FCS files in R. Let us know if you'd like to request this feature be built into the Cytobank application.

 

Behind the scenes

  • When will my task be completed?

Advanced analysis runtime can vary depending on the number of files, events, channels you are analyzing, as well as your selected algorithm settings, such as iterations. (Tip: Set up a small pilot run to see if you expect to see any interesting results before running a very large viSNE or CITRUS analysis. That way, you can tell quickly if your analysis will give you interesting results.)

You can monitor the progress of all your ongoing analyses in the Recent Tasks section of your Experiment Manager when you log in to your Cytobank account.

You will receive an email notification when any of the following tasks are completed: Export Statistics, Export Events, Export ACS, SPADE, viSNE, CITRUS, and FlowSOM. 

  • Why is my experiment “in queue”?

Your Cytobank server may be used by multiple users. When you run an advanced analysis, your request will be sent to a queue. If you are the first user in queue and the server does not pick up the task accordingly, most likely the background computer in the cloud needs time to turn on, which normally takes 10-20min.

By default, each Premium user is restricted to run up to 3 simultaneous advanced analyses at a time to avoid traffic jammed by one person and to enable sharing of resources with other active users on the same server. If you set up more than 3 analyses, they will each begin as your previous runs complete. On Enterprise Cytobank, the limit of simultaneous runs per user, as well as total runs across the server, can be customized to reduce queuing time.

 



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