The Daily Dongle

FlowJo on OSX 10.8, and the "Do you want [...] incoming network connections?" dialog

These dialogs occur sometimes during FJ startup on OSX10.8 macintosh machines. Typically you will get the "java" one, and if you add java to your allowed firewall entries, it will ask about flowjo. In my experience these dialogs are sporadic and transient, automatically disappearing during startup. This does not seem to affect FlowJo. 

 

 

Plate Tool in FlowJo Vx

Staring with this week's beta, Layout Editor has a cool new plate tool that allows visualization of a plate-worth of data as heatmap, split heatmap, or Chernoff faces. This utility is not to be confused with the Plate Editor platform.

 

tip for roaming profilers

as we learn more about structured Windows setups in various institutions, its becoming clear that roaming profiles are not gracefully handled by FlowJo. Namely, we're assuming write priviledges when we may not have them. 

If you are dealing with this issue, the solution is to modify flowjo's LAX file, which is created by the installer process in the same folder where you installed flowjo (ex. c:\program files\flowjo10\flowjo10.lax ). In notepad, go to the bottom of the lax file, and in a new line, add

lax.nl.java.option.additional=-Duser.home=Z:\\Profiles\\FlowJo Vx\\

replacing my path with yours - and then starting up FlowJo to confirm it worked. 

problems with batching saving to excel

Due to our re-packaging a 3rd party library that we rely on for this functionality, 10.0.6 release had an error where the new library was included but was referred to by its previous file name. 

Long story short, if you can't batch/save to excel in this version 10.0.6, simply re-download FlowJo. I reposted the same installers from the shipping version of March 25th that correct the naming issue for this particular library. 

Tests were added to release procedure to ensure we dont miss this (or similar) mistakes. 

FlowJo Reference Reloaded

Vx manual has been largerly reorganized, and many of the sections rewritten. This is continuting to tutorials now. So, in addition to the youtube tutorials we've posted about previously, check out docs. 

http://docs.flowjo.com/

Ribbons PSA

As new users switch from V9 to Vx, we continue to get the occasional "grumbles, ribbons!" email. Here are some quick and easy ways to get those pixles off your screen, unless you need them. 

Cytometer Prefs and Data Scaling

In FlowJo Vx, by default, we will scale data parameters based on the keywords in your data.

In some use cases, FlowJo users wish to alter these scales. We introduced storing these in preferences in V7, but it was done in a global way, meaning if you "tuned" your settings for Accuri data and then went on to Cellquest files, scaling would not look good. Worse, preferences were matched to parameters based on name strings, so if you had a custom transform for "FSC-A", which is commonly used across multiple vendors, you would be affecting all of them. 

FlowJo Vx 10.0.6 beta

this version shipped. you can download it now as "10.0.6" from flowjo.com;  beta testing of 10.0.7 will resume some time soon. 

Speed tricks for analyzing Large Data Files

Some flow researchers with large event count files, ask us for tips to speed up the FlowJo analysis. Here are a couple quickies.

Preprocessing

If the analysis workflow allows it, one can do some pre-processing. In FlowJo, gate on Cells of interest (eliminating debris and doublets), then use the Export feature to create smaller fcs files.

Ram Disk

One can benefit from setting up a RAM disk, especially if the fcs files are  greater than 10MB. (If you need more RAM for your Mac, check out www.crucial.com). On MacOSX, one can mount a 2Gig RAM Disk easily by pasting the text below into Terminal:

diskutil erasevolume HFS+ "ramdisk" `hdiutil attach -nomount ram://4000000`

Or one can use a program like Tmpdisk to create a RAM Disk.

Make sure you create a folder on the RAM disk for your flowjo workspace file and fcs files (loading the fcs files into flowjo from the RAM disk), and copy the RAM Disk folder to your hard drive when done with the analysis.

OSX 10.8 and zip file blues

if you are on one of them fanshy upgraded OSX 10.8 computers and hit an error about a "corrupted file" when accessing one of our downloads in Zip format, apparently you have to go to Security/Privacy OSX preference panel and click as arrowed below: 

 This will enable your ability to deflate our Zip files.