Flow Cytometry User Group Meeting – 8th August 10am – Conference Room C2.22.
We would like to revive the Monthly Cytometry User Group meetings as a forum where users can discuss cytometry related problems, issues, triumphs and successes.
This will be an open forum where users are encouraged to bring data along to share and work through.
The first one will include “Cytometry Tips & Tricks” as well as some discussion in regards to building/sharing core panels to be utilised across labs.
When: August 8th 10am-12pm.
Where: Level 2 Conference Room, WIMR.
What: Cytometry Tips & user discussion.
Did you say colourful? BD Symphony is outputting high quality data.
The Symphony is ready to use! The instrument has been used by a number of researchers with positive feedback. The current configuration allows for at least 34 (yes 34) different fluorescent dyes to be detected in addition to 3 scatter parameters. Be sure to check out the current configuration listing the non-exhaustive plethora of dye choices.
Why would you want to use it? Well, if you are having trouble choosing fluorochromes for your panel, the increased options certainly may help, or if you are finding it difficult to find time on the Fortessa/LSRII, all currently utilised flurochromes can now be detected on the Symphony ensuring an event-free (*no pun intended*) transition. The additional scatter parameter can help also increase dynamic range allowing both small and large particles to be detected simultaneously.
Training takes ~30minutes if you already cytometer access and requests are accepted through PPMS.
Spectral Unmixing - Improve your population resolution…
FlowJo 10.6 was released yesterday (after months of beta testing)! This update allowed weighted non-negative least squares fitting for spectral unmixing of your cytometry data!
What does this mean… Instead of compensating your data, you can now spectrally unmix, essentially using all the detectors as reference points for the fluorochromes spectra.
You will need too (and should have been already) ensure all instrument detectors are active and collecting signals as well as ensuring all signals are not off scale for non-primary detectors.
The process is almost similar to compensating using FlowJo but just involves clicking 2 more items in the software when compensating your data.
And you guessed it – this is where the Symphony excels with its numerous detectors.
The shared data analysis computer has had the upgrade but see here for further information.
Additionally this can be performed retrospectivly on standard cytometers if the data was collected with additonal detectors enabled.
Example spectral data - BV737 detected across many detectors.
Fancy Using A Supercomputer? I did (and loved it).
Argus is the University of Sydney’s “Virtual Remote Desktop” project designed to bring remote, on-demand, interactive, graphically intensive compute environments to researchers.
Westmead Cytometry & Westmead Imaging now provide access to 3 of these systems for you to access for those compute intensive applications. These remote desktops are fast. Each system has 16x XEON core CPUs and an impressive 128GB RAM alongside 8GB GDDR5 NVIDIA GPUs with network throughputs of 200+ GBPS. NBN is 1GBPS for comparison.
The Argus team (special thanks to Ashok Pachipala @ USYD) have installed all of the right applications including R, RStudio, Huygens, ImageJ, CellProfiler, FlowJo(T&Cs apply), Office, AutoCAD and others making it an excellent desktop to log into, setup something that will take a while (tSNE, Image Deconvolution, etc), and let it do its thing.
Access is easy, all that is required is a Unikey and a return email acknowledging some basic guidelines. Booking is via PPMS and shhhh… they aren’t charged. These desktops have proven so capable that they even have altered mindsets of purchasing new analysis PCs.
Have Something You Need *3D* Printed?
A reminder that we have a 3D printer that can be accessed by all researchers. It has proven very capable with a number of useful prints having been produced to date. Slide holders, electron microscope parts, centrifuge parts, kidney transplant mounts, and a build your own cytometer. If you have a requirement for a custom designed novel scientific part that will assist your research, let us know!
More information can be found here
An Automatic Plate Washer!
It has been brought to my attention that many researchers are in the dark that we have an automatic 96 well plate washer available in the flow labs. If you could use this for plate based assays, such as ELISA’s, or protein quantification assays, then it is very easy to use. If you would like to be trained to use it training requests are through PPMS.
For a complete list of instruments available at Westmead Cytometry click here
Cell Counter - Now Available – Give It A Try.
Still counting PBMCs or splenocytes manually?
The cell counter can also. 50uL and ~<1min/sample.
The newly installed CytoFLEX (2 laser, 4 parameter) flow cytometer is available to use @ Westmead Cytometry. The instrument can be used as an accurate cell counter providing researchers with an accurate, quick, accessible cell counter to utilise in your research. The instrument doesn’t require booking and training is via key superusers located across the WRH. In addition to cell counting, parameters such as GFP expression, viability and scatter profiles can be collected. The instruments accepts Eppendorf tubes and 5mL FACS tubes, requiring 50uL and ~40seconds per sample. Facility provided DAPI and Syto Dyes are available also.
Key SuperUsers who can be contacted for training/further information include:
Suat Dervish
Edwin Lau
Ya Wang
Joey Lai
Cindy Zhu
Stephen Schibeci
Daniel Hu
Nicole Fewings
Cyto2019 – Vancouver - Abstract Submission Is Now Open
Cyto is unquestionable the most prominent cytometry research conference internationally. Cyto2019 will be held in Vancouver, June 22 – June 26 – 2019.
Submit an abstract before February 11th for your opportunity to present your data to an audience of cytometry/immunology/many discipline experts (an eclectic bunch). Just as important is what can be gained from the conference, i.e. the latest in data analysis workflows /algorithms, latest reagent/assay information, and sneak peaks of novel disruptive technologies entering the cytometry space. Travel awards are available for eligible applicants.
Scientific Platforms Data Clean Up Reminder
Some of you are probably using the Scientific platforms drive to store you exported flow data temporarily. As the drive is getting full, we will have to clean up the drive according to our data policy: All data >14 days old will be deleted.
On 15/2, IT will be deleting data files on Scientific Platforms that are more than 14 days old automatically. Please save all wanted files onto your local storage.
If you have any concerns please contact us.
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