The Daily Dongle

new mac beta

The currently posted b6 will expire in 6 days. This new b7 (download) will expire in two months. Bug fixes/improvements since b6:

(1) Fix: The TE statistic "Freq. of" (a subset) now works when iterating by keyword (previously, it was left blank)
(2) Fix: "Live" attribute for groups is obeyed when you select to create multiple gruops from panels
(3) Help: when defining a custom transformation on data with a huge negative range, FJ doesn't accommodate all of the negative values and makes for a better transformation.
(4) New: Remove custom transformation menu item
(5) New: Checkbox in "Edit Compensation Matrix" dialog window -- when selected, all stats in the current group in the WS are forced to recalculate whenever the matrix is changed -- allows better editing based on stats

mens flowjos

Thanks to JQ for the link    - click here - not that we'd recommend open-toe shoes for anyone working with blood, or blood-derived cells :)

algorithm for FlowJo's sample validity platform

Since many users asked, engineering and FlowJo owners agreed to release the details of our validity platform.

I've just included that detail here:
http://www.flowjo.com/v8/html/validitydetails.html

and updated the main validity page to also point to this resource. http://www.flowjo.com/v8/html/validity.html

adding vocabulary to command-line-flowjo

Cool extension to the growing feature set collectively known as "command line flowjo" (CLF), thanks to Jay. This specific feature will probably be included in the 7.6 series (we're still working out 7.5 'wrinkles').

The existing CLF switches in 7.5 allow users to create batches of flowjo analyses - which take arguments of template file and folder of data, and whether to quit, save, batch, whatever else - including creating file output like powerpoint batches or quicktime movies and excel spreadsheets. Neat. 

In 7.6 Jay also added the ability to batch-export or batch-concat samples/gates.. 

This is really good news if you have 12Honkabyte files who need deflation into only those in gate B, but for 50 data sets. The type of stuff you can setup in a template and leave running overnight (data pre-processing ? )

From Jay's email:  

It is now possible to perform the export/concatenate operation on a group, in addition to an individual population.  This is performed by selecting the group and using the right button popup menu to 'Group Export/Concatenate...'.  This opens the usual Export/Concatenate Dialog, but the operation will be performed on all samples in the selected group.  You can also select a group-owned sub-population to perform this operation.  When this dialog is opened, there is an additional checkbox in the dialog, to indicate whether you would like to save the export/concatenate operation with the template.  If this checkbox is selected, then the template stores additional information to perform the export/concatenate operation when the template is opened using the command line invocation.  It is hoped that this will provide the necessary functionality to build automated tests for the export/concatenate operation.

Here is how it works...

Create groups with ownership criteria so samples will be assigned to the groups automatically.

Create group-owned gates as needed.

In the Groups panel of the workspace, select a group-owned gate, popup the right button menu and choose 'Group Export/Concatenate...'.

Select the checkbox to 'Save with template'.  Select 'Concatenate' if so desired.

Click the 'Export' button to perform the operation.

Perform multiple export/concatenate operations on different groups or subpopulations, as needed.

Now save the workspace as a template, and quit FlowJo.

Now start FlowJo using the command line, with two arguments: the full path and name of the template file (you should probably enclose the path with double quotes), and the full path and name of a folder of data files to load (again, encloses in double quotes).

After FlowJo loads the template, it will perform all export/concatenate commands, placing the newly created files in the same folder where the template is stored.

Feedback welcome...

new way to set number of decades on log plots

In an upcoming Mac 8.9 release, this dialog (FlowJo > Prefs > Workspace > Define..)  has new clicks:

Specifically in the middle section called "Standard Log Conversion Settings" :

The Setting-Formerly-Known-as-Starting Linear Channel Number is now simply called "lowest". This setting, in the units of channels, controls the left edge of the scale. If you type in 1000, you will chop the first 1000 channels from your data, and it will start at 10^3 instead of the usual 10^0.

The new setting, "highest", is in the units of decades. If you leave it at 0, the max value of the scale stays at what it was originally (for example, Accuri files go to 7.2 decades, diva - 5.4, etc.

Notice that the two settings are mutually exclusive.

The second control after you pick your left or right edge, is the number of decades in the "pulse area/height" text fields.

In the screenshot shown, I'm setting my prefs for Accuri data. I want to shave 0.3 off the top (assuming my fluorescence range usually doesn't hit the max value) and show what's left as 5 logs. Which would look like this:

Which looks more manageable than the full scale:

Look for the 8.9 beta, out now. 

FlowJo translation project

We're starting to translate FlowJo into other languages. Please leave a comment on this post if your language should be added to the list. Currently we are making progress in Chinese and Polish (we just happen to have prolific translators fluent in these, as well as German and French, which will likely be next.)

 Anything else?  

We might be interested in translators for languages other than the four mentioned - unicode experience is a must. Let us know if you'd be into it, and maybe we can discuss how to make it worth your while (probably limited to feel-good-points and T shirts.) FlowJo pratar inte Svenska!