RE: making figures from facs histograms - did I miss something
From: J.Paul Robinson (jpr@flowcyt.cyto.purdue.edu)
Date: Tue Jan 09 2001 - 23:56:36 EST
OK I give in....where are you Mario....surely the MAC software is
the publishers dream....it can't be as horrific as all these messages
suggest....(although I did note its really interesting changing the
axis label in cellquest...) did I miss something ...
Paul
: Calman Prussin <CPRUSSIN@niaid.nih.gov>
To: cyto-inbox
Subject: RE: making figures from facs histograms
Date sent: Tue, 9 Jan 2001 03:51:28 -0500
It amazes me that 5-6 years after the development of CellQuest, BD has never
published a primer on "Publishing with CellQuest". Several years ago I asked
a BD researcher a similar question of how they make their beautiful slides
and got a "minimalist" answer. I would like to see a BD representative
address this question or better yet...publish a primer.
It is too late a night (or I am too lazy) to put my own Cellquest to Canvas
methods to keyboard. But my general thoughts are that screen dumps are not
the way to go.
I use Canvas because I am fluent in its' use, not because I think it the
best program. If I had to learn it fresh, I might consider Adobe
Illustrator. What I would like to see in any publishing/graphic procedure:
1. Excellent resolution
2. Ability to rename axes, add arrows, labels
3. Ability to change the color of the dot plot.
Number 3 is very important to me for slide making, as rare events are
difficult to see with black on a white background. I use yellow on a dark
blue background. I did not see mention of that capacity in any of previous
emails (can they do it?). Canvas gives you all of those.
Calman
> ----------
> From: Idit Hazan
> Sent: Wednesday, January 3, 2001 5:37 PM
> To: Cytometry Mailing List
> Subject: making figures from facs histograms
>
>
> hi
> does anyone know how to convert the histograms that come off the
> Cell-Quest
> program into something that can be copied and pasted into a graphic
> software (such as adobe or canvas), in order to make complicated figures?
> i was told cell-quest in not very user friendly and that people print
> their
> histograms, then scan them and use the scans as graphic files. there has
> to
> be a more elegant way...
> Idit Hazan
> University of California, Irvine
>
>
J.Paul Robinson, PhD PH:(765)4940757
Professor of Immunopharmacology
Professor of Biomedical Engineering
Purdue University FAX:(765)4940517
EMAIL:jpr@flowcyt.cyto.purdue.edu
WEB: http://www.cyto.purdue.edu
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:03 EST
RE: making figures from facs histograms - did I miss something
From: Mario Roederer (Roederer@drmr.com)
Date: Thu Jan 11 2001 - 15:36:20 EST
At 11:56 PM -0500 1/9/01, J.Paul Robinson wrote:
>OK I give in....where are you Mario....surely the MAC software is
>the publishers dream....it can't be as horrific as all these messages
>suggest....(although I did note its really interesting changing the
>axis label in cellquest...) did I miss something ...
Paul (etc.):
Unfortunately, CellQuest was never written with the generation of
publication quality figures in mind. Hence, all of its displays (as
far as I can tell) are "bitmap" representations, with no vector/font
information. Hence, it is difficult to change things like colors,
fonts, etc.--you must use a program that can do bitmap editting and
then overlay with your own text/line information. (Witness the
contortions people have to go through to make publication-quality
graphics!)
Paul was baiting my response about FlowJo and Macintoshes, so here
goes. FlowJo was indeed designed to do publication quality output
(although not necessarily directly from the program, albeit it is
possible). Not only do you have great control over the images (font
usage, font styling, overlay colors, addition of graphical elements,
text elements, annotations, etc.), but all images can be exported in
either JPEG, GIF, TIFF, or PICT format. The first three formats,
while useful for sending to PC's and publishing on the web, are
essentially bitmap representations (although high-resolution,
publication-quality). However, the PICT format, which is the
Macintosh standard for graphics, gives you complete control. When
you copy from FlowJo and paste into any graphics application, you can
then ungroup the elements, select individual lines (or contours, dots
in dot plots, etc.), text items, or whatever, and manipulate them at
will.
For some examples, see
<http://www.treestar.com/flowjo/v3/html/pubgallery.html>. For other
examples, see any of my publications... in particular, I'd like to
take this opportunity to advertise the upcoming February issue of
Nature Medicine, in which we have a New Technology article about
11-color flow cytometry!
The nice thing about Macintoshes is (as Paul notes) their power in
publication. You can easily copy and paste between nearly any
applications, and, if they follow the PICT format, in a way that
preserves grouping of objects, fonts, vectors, fill patterns, bitmap
images, etc. etc. By the way, I second the suggestion previously
made on this list regarding "GraphicConverter". This is an
oustanding program that you can use to interconvert between nearly
any graphics formats. It is shareware, written by Thorsten Lemke in
Germany. See <http://www.lemkesoft.com/> for information.
mr
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:03 EST
FW: FlowJo Seminar for Los Angeles Basin
I'm not sure if there is a Los Angeles Basin users group,
but thought I could advertise here to interested parties.
Thanks,
Lora Barsky - Lead Operator
Research Immunology/BMT FACS Core
Childrens Hospital Los Angeles
> __________________________________________________________________
>
>
> FLOWJO TUTORIAL SEMINAR
> Presented by Jennifer Wilshire, Ph.D.
> Friday, March 30th
> 11 A.M.- Noon
> Room 200, Smith Research Tower
> Children's Hospital
> __________________________________________________________________
>
>
> 11 A.M.- Noon - Demonstration, Q+A, and discussion of
>
> 1 - 5 P.M.- Personalized consulting (GoFlowJo@yahoo.com for an
> appointment)
>
>
> *
>
>
> On Friday, March 30th, Tree Star, Inc. will offer on-site training
> sessions on using FlowJo for the analysis of flow cytometric data. FlowJo
> is advanced offline data analysis software, originally designed at the
> Stanford Shared FACS Facility, and now commercialized and in use by
> leading research sites worldwide.
>
>
> Built into the program is a wide array of visualizations and gating tools,
> as well as special platforms for Calcium Flux analysis, Cell Cycle
> analysis, Proliferation analysis, Population Comparison, Quantitation, and
> Compensation. FlowJo produces the best publication quality graphics
> available, and introduces new technologies for presenting and publishing
> flow data via the web.
>
>
> Please visit <http://www.flowjo.com> for more information or to download a
> free 60-day trial of FlowJo. << File: Flyer good-USC >>
>
> <<Flyer_good.jpg>>
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