CSC Bioinformatics

ΔThis page is still under constructionΔ

The CSC has specialized software for advanced image analysis. In summary: Harmony is the image controller software for the Phenix microscope and it performs analysis too (one plate at a time) – this is available on an additional analysis workstation that is remotely accessible by users and is linked to the Phenix itself. Meta Xpress is the image 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 desk, and are accessible remotely via TeamViewer. Signals Image Artist is an analysis software that can analyze multiple plates at a time quickly. It is capable of interfacing with the Harmony and MDCStore (for Image Xpress) image databases to fetch images for analysis. It runs on a Linux computer in the lab, and is accessed via a web portal. Spotfire is used to perform advanced statistical analyses on the data from Signals Image Artist, as well as our own HistDiff, which is used for multiparametric comparisons to measure how different two datasets are. We also have other in-house created tools and other resources linked here.

I. HistDiff

II. Spotfire

Spotfire is a software for visualizing and performing calculations 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 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 subscription for 5 years.

III. Signals Image Artist

To access this system, see the steps outlined in detail in the protocol linked here.
“Signals Image Artist (SImA) is the universal high-volume image data storage and analysis system that enables fast and secure access to images from a large number of sources via the internet. The SImA system lets scientists remotely access, view, annotate and analyze images from anywhere in the world. It is easy to use and can serve multiple users simultaneously, making it perfect for any size user base, from an individual lab to an entire organization.” — Perkin Elmer

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 Perkin Elmer via their support website
  • email informatics.support@perkinelmer.com

IV. Harmony

  • Here are instructions for remote desktop connecting to our Harmony workstation. Note that this workstation is currently good for viewing images, designing an analysis sequence, and looking at numerical data, but is pretty slow when doing an analysis run, especially if there are many sites/wells/channels. If you are doing a timecourse tracking, or an analysis in 3D, then it pretty much won’t go at all.
  • 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)

V. MetaXpress

VI. MDC Store

VII. Other tools