The Daily Dongle

working on tab delimited text files -> flowjo

One of the very first posts on the DD, and one of the most frequent - and oldest- of feature requests, is to read in non-flow files into FlowJo. Currently the mac version sort of does this, but you have to hand-write the text header. 

I think we can improve that by just supporting any (for starters, tab delim'd data) 2D array text file and figure out the ranges on the fly. And even make an FCS file out of it. I hope to have a demoable prototype before CDW. For now I'm limiting my scope to 10bit FCS2 format (bigger/smaller data will be normalized to "fit" in ten bits).

update on my DVS post

I just got a few minutes of Scott Tanner's time to get some more details about what/when/how/who, and would like to append my earlier posting.

On the question of "maturity" of the cyTOF machine:

"As a conservative instrument developer, I'd never say a product was mature until it has been operated by a colony of C Elegans for 4 years without fault.

 The CyTOF is now stable and ship-able (we just received the required CSA, UL and FAA approvals for shipment into the US).  We will be shipping two pre-commercial instruments in October.  And we are ready to receive commercial orders: we will be formally launching the CyTOF at the GLIIFCA meeting at weeks' end.  "

On the question of "touring/demoing" the cyTOF machine:

We do not have plans to send the instrument itself on tour: we invite interested (and hopefully interesting) people to visit us in Toronto.  Two recent visitors were operating the instrument by themselves within a couple of hours, and one commented that it was already more stable and use-able than many commercial analytical instruments (his comment: if we were in the US, we'd already be shipping these things...).

8.9b13

http://offsite.treestar.com/downloads/fjbeta.zip

- fixes "wrapping" problem reported by some users (bottom of FSC wraps to top of FSC)

- implements SVG/Intaglio support

demo - Population Comparison in 7.6

Quicktime post - 6.1MB, ~2 min demo of the PopComp platform in the Java version of FlowJo: 

(click picture to access movie)

Dear Readers.

Thanks for reading.

It appears the Daily Dongle now draws 1200 visit(or)s per week. There are about 4 years worth of tutorials and tech support Q&A type stuff on here. While those of you who express the Google Gene probably have no trouble finding the right content, I wonder if there is a way to organize and/or index this blog better.

I'm impressed at how H. Maecker reinvented his blog and I'm looking into something similar for the Double-D.

I also wonder how you, the CSS regulars, feel about Daily Dongle shwag? Would you be into a $10 T Shirt with something DDongly to help pay rent? Or a freebie at a tradeshow alongside the usual FlowJo goodies?

Comment y'all, otherwise I'll know it's just 1199 textbots and me reading ;)

V 7.6 (re)learns Accuri Cflow generated data

Picket fencing is no more! Thanks to Jay's work we now look at the Maxusefulchannel keywords inside Accuri data. Assuming this was properly set to match your data's distribution inside CFlow, FlowJo should pick up the range and scale the data accordingly, automatically, and without deriving parameters (or the resulting picket fencing.)

I've exhausted my limited set of Accuri files, and accidentally deleted my copy of CFlow, so while I recover that, if any of you (with accuri picked fencing or data-scaling problems) want a preview of this, as a beta build, please email simm@treestar.com

DVS CyTOF now on tour

Few years back I reported back from CDW about the intriguing plasma-torching, Lanthanide-tagging their antibodies, 50+ parameter "cytometer".

Well, So now, Scott Tanner's group has a nearly-mature product, and are touring around your local flow-show. I've read they'll be at GLIIFCA and Alan Saluk's optical thing in Southern Cali. Google it, or contact DVS Sciences - to find out if you can demo one near your location:

http://www.dvssciences.com/

V8 learns SVG

FlowJo V8 will soon have a new beta which implements SVG support. 

We've been working with Intaglio to ensure cross-compatibility. Intaglio is a great tool for graphics laundering, or vector figure-making. 

CS4 also supports our SVG, but it seems that Illustrator has a "interpretation" rather than "implementation" of svg. We test ours vs http://www.codedread.com/svg-support.php and illustrator sometimes does not match the rendering 100%. 

Still no good news for keynote/PPT2008+, but we're keeping our eyes and ears open for solutions. 

flower to the people

 flowSTRONG bands - 2GB data storage. Ask your local apsci at a trade show near you!

BD's multicolor flow utils

http://www.bdbiosciences.com/research/multicolor/tools/index.jsp

neat!