CSC Bioinformatics

ΔThis page is still under constructionΔ

The CSC offers specialized software and tools for advanced image analysis.

The flowchart shows that imaging is by the Phenix (takes all specimens) or IXM (only fluorescent microplates). IXM data is analyzed by MetaXpress on the IXM workstation or on Signals (remotely accessible). Phenix data is analyzed in Harmony (on either Phenix PC or Bioinformatics PC - the latter of these is remotely accessible) or Siganls.
Above is a flowchart describing how a user progresses through the available imaging systems and analysis platforms, and how they are interconnected.

Of the analysis platforms detailed below, the fees associated are per hour of use on either the Phenix PC or the Bioinformatics (Harmony) PC) and image data storage on the Phenix PC (per TB per month).

I. Harmony Software

Harmony is the image controller software on the Phenix microscope. It performs analysis too, one plate at a time, which can be queued to run concurrently with imaging. The analysis functions are also available on an additional analysis workstation (a.k.a. the Bioinformatics PC) that is remotely accessible by users (please use the FACES signup calendar!) and is automatically linked to the Phenix’s image database.

  • Here’s a YouTube video with basic training on Harmony: https://www.youtube.com/watch?v=G4PrLdJvsRc&list=PLwtH3MqBsI97tajOpWgKMVAN1pbE477XV&index=2&pp=iAQB
  • Here are instructions for remote desktop connecting to our Harmony workstation. Note that new users need to be added individually first, to be able to connect remotely.
  • Please expect the Harmony workstation to be pretty slow when doing an analysis run, if there are many sites/wells/channels/timepoints/slices, and worse if analyzing with “tracking” or in 3D space. The Phenix PC will be a bit faster in those instances – consider letting it run overnight or over the weekend and I can reduce the price of the session if you let me know your situation.
  • How to archive data from just a subset of your wells, e.g. for sharing with Perkin Elmer reps when you need help designing an analysis sequence.
  • a white paper about 3D analysis in Harmony and Signals Image Artist (6 pg PDF)

Here is a screenshot from Harmony doing timelapse growth curves:

several growth curves in the context of an interface that has a data table and well selected and fields of view outlined

II. Signals Image Artist Software

Signals Image Artist is a high-volume analysis software that can analyze multiple plates at a time quickly. It is capable of interfacing with the Harmony (a.k.a. Columbus transfer) and MDCStore (for Image Xpress) image databases to fetch images for analysis, and transfer can be queued concurrently with imaging on the Phenix. Note that Harmony analysis settings can also be exported and loaded onto Signals, if you want to use the Harmony interface to build it for ease of use. It runs on a Linux computer in the lab, and is only accessed indirectly by users via a web portal. The computer contains a sizeable drive designated mostly for long-term storing of cytological profiling reference data.
To access this system, see the steps outlined in detail in the protocol linked here.

Supported Image Data Formats (accurate as of v1.0 Sept 2021):

• PerkinElmer Opera Phenix, Operetta CLS, MuviCyte, Columbus

• Molecular Devices MDC Store

• Molecular Devices Metamorph

• Yokogawa CellYoyager

• GE InCell

»Video of our training session hosted by Perkin Elmer with how to use Signals Image Artist for image segmentation.

Further information:

  • Official YouTube channel for PE bioinformatics has some informative videos
  • PE sales website with Signals Image Artist information and several videos
  • Brochure with a short summary of Signals Image Artist features (3 pg PDF)
  • Release notes (5 pg PDF with common issues/workarounds)
  • Installation, configuration, and administration instructions (23 pg PDF)
  • REST API (18 pg PDF incl. token authentication info, about image downloads, and shortcodes)
  • how to connect an external SLURM cluster to SImA (22 pg PDF)

Contacts for support:

  • contact Revvity Perkin Elmer via their support website
  • email support+id273120@revvitysignals.zendesk.com.

Here is an image of the Signals Image Artist window:

III. Spotfire Spoftware

Spotfire is currently only available by appointment with Beverley (requires their login credentials).

Spotfire is not for image quantification, it is software for visualizing (e.g. heatmaps) and performing calculations (e.g. clustering) on large datasets. Here are some tutorials on Spotfire:

  • 18 min YouTube from Spotfire incl building an analysis using natural language! Type what you want to know (e.g. which concentration had the biggest effect?) and it will populate some example visualizations for you to pick from. It uses machine learning to find related variables that it suggests as being useful for addressing your question.
  • Slides of screenshots from Spotfire Quarterly Connect session(s). These are webinars hosted by Revvity (Perkin Elmer) to help new users get started. We’ll try to let the users know in advance to register and attend these webinars, but some of the info will also be captured here in the slideshow for your reference. These slides are visible to anyone logged in to Google with a CruzID.

You can access example analyses in the library. One example opened on our system is below:

screenshot showing a histogram and dose response curve and plate map

Note that Beverley’s CruzID was used as the initial login to the server to activate the software, and will be needed for updates in future, otherwise it can be switched to “offline mode”. We only have single-seat subscription for 5 years.

IV. MetaXpress Software

Meta Xpress is the imaging controller software for the Image Xpress microscope and it performs analysis similar to Harmony (one plate at a time). This is available on a total of five computers at the ImageXpress workstation, and are accessible remotely via TeamViewer. The images captured by MetaXpress from the Image Xpress are automatically saved in a databased called the MDC Store, located on one of the four PCs that are separate from the device controller PC.

V. HistDiff

Our in-house system called HistDiff is used to combine single-cell data into one score for each measurement.

VI. CSC Image Viewer

A tool for easily retrieving the images associated with our datasets. Only those that have been processed through HistDiff, and subsequently sent to Image Viewer, are visible at this time. Simply perform an advanced search for the treatment of interest (e.g. common name for a drug) and you will see the images from those wells.

https://cscimageview.ucsc.edu/

VII. QC Gaultlet

A new tool for showing activity scores, designed to identify plates with outlying control wells.

VIII. MOAST

A tool in progress for assigning the mechanism of action through guilt-by-association analysis of images compared with a reference database of images for known bioactives.

IIX. HiTS database

This is a collaboration with UCSF.