Tuesday, May 6, 2008

Clinical and Research use of Photoshop CS3 Extended

My article "Photoshop CS3 Extended Tools will help save lives" was published in the September Issue of Photoshop User Magazine.  This is the first entry in the new column Photoshop CS3 for Research.  

I introduce some general uses of Photoshop in microscopy and other research examples including soft agar colony analysis, medial cerebral artery occlusion mode, and DICOM importations.

The content is provided courtesy of Photoshop User magazine (www.photoshopuser.com)
To read the article click here.


Friday, May 2, 2008

From Photoshop User magazine - CS3 Analysis Overview

I recently got permission to post my articles published in Photoshop® User Magazine. This is my first article for NAPP found in the special Summer Issue on Photoshop CS3. I hope you enjoy it. It goes over the  analysis features added to Photoshop CS3 Extended. 

The content is provided courtesy of Photoshop User magazine (www.photoshopuser.com)
Clicking here will take you to a readable version of the article.

Tuesday, February 12, 2008

Available - Photoshop CS3 Extended for Biomedical Research Training DVD

Now you can have Photoshop CS3 Extended training dedicated to helping biomedical researchers.

After two decades of working in drug discovery this is the training I needed to do my job better. Many years ago I looked for a title that would help me conduct research and apply Photoshop better. Almost none of the training available was developed by fellow researchers. So I created something that helped me and can help you understand imaging basics, learn Photoshop CS3 Extended capabilities, and see actual workflows.

To view this valuable training you can either subscribe to lynda.com. This will give you access not only to my title but titles from well over 100 other authors covering software, graphics, design and a multitude of other subjects. Starting at $25 a month it is a bargain for on demand training. Or you can simply purchase my training DVD.

The direct link to purchase the Photoshop CS3 Extended for Biomedical Research DVD is http://www.lynda.com/store/ProductInfo.aspx?productid=680

Photoshop is software that helps researchers get the most out of their images. Whether using it in conducting research, creating presentations or aiding communication we all can learn to wield this tool better.

I hope I have helped fellow biomedical scientists by creating and sharing this work.

Take care

Eric

Saturday, January 26, 2008

Lynda.com launches my Photoshop title




On January 25th Lynda.com launched my training course, Photoshop CS3 Extended for Biomedical Research. I go into detail how Photoshop CS3 Extended can be used in Biomedical Research. This is based on over fifteen years of drug discovery experience including the creation and managing of a digital darkroom for DuPont Merck and later Dupont Pharmaceuticals.

I cover how to use Photoshop CS3's selection, analysis, and editing tools to evaluate an image's color composition, modify images for research, optimize exposure with levels and curves, transform images with layers, and compensate for acquisition problems and limitations. I also explain how to add reference information to images, annotate and optimize DICOM animations, and share finished images with colleagues. If you are a Lynda.com premium subscriber you have access to exercise files that accompany the tutorials.

I hope that I can help fellow researchers use Photoshop to help them in their studies and demonstrate how it can be a useful tool at their disposal.

Friday, January 11, 2008

The Drobo saved my "life"


Most of us keep a substantial amount of our life on our computers. Current work, personal information, contacts, bookmarks, and the detritus that make up a modern life reside as ones and zeros in a magnetic state in a box nearby.

Now there are only two types of computers in this world. The first group are the computers that are broken and don't work. The second group are the computers that will break and won't work, usually at the worst possible time.

Because this is the way of all things, having a current backup of your hard drive is essential to "life" or at least a good nights sleep.

My Drobo has become a part of good data management. I conduct regular full HD backups using Superduper to backup my entire hard drive once a month (data once a week). With the 1.3 TB of hard drive space (2 x 750GB, 300GB, and 400GB Drives) I can have everything in a one place. When my Macbook Pro went down between Xmas and New Year's I was able to attach my Drobo to my 7 year old G4 install some applications and continue to work.

My G4 is not as stable as my MBP was. It crashes/freezes about every other day but my Drobo has kept my data protected.

My MBP has been at the Apple repair facility since 12/28/07 repairs on hold waiting for a part. Until it get sent back my G4 and Drobo are managing fine if not quickly.

Tuesday, January 1, 2008

My 2007 - A Good Start

As we start the new year it is always good practice to review the last. As I transitioned from Bristol-Myers Squibb Medical Imaging to independent consulting I can share my accomplishments that set the foundation for 2008. Below is the summary of some of my work that I would not have been able to accomplish without the help of many individuals that have given me opportunity and support.

Just to name few are:

Dr. Joseph Bailey for DICOM training, moral support, and a great friendship.

Pamela Pfiffner for the patience, direction and training materials.

Dr. Simon Robinson for honest feedback, supervision and continued support.

Chris Mattia for the help and direction in the taping of my Lynda.com titles.

Folks at Adobe for the chance give input and training to others on the use of Photoshop by Biomedical Professionals

NAPP staff for the support and training as well as the opportunity to conduct training at Photoshop World and in Photoshop User magazine.

My wonderful wife whose support, proofing, and editing of my work has improved the quality of my material and has made it possible to start doing training and consulting.



2007 Accomplishments


1) Member of Adobe’s Biomedical Image Advisory Group
September 2006 - Present
http://wwwimages.adobe.com/www.adobe.com/products/photoshop/photoshopextended/medical/pdfs

2) eSeminar for Adobe – August 14, 2007
Currently available on Adobe’s onDemand webpage – Photoshop CS3 Extended for Scientific_08_14
Photoshop CS3 Extended for Science and Medical Imaging
Tuesday, August 14th, 2007 9:00 A.M. PDT. 12:00 P.M. EDT
In this seminar, we will demonstrate new selection, measurement, and analysis tools that let you quickly extract and export a wide array of quantitative data from microscopic and radiological images, including native support for DICOM images.

3) Adobe Success Story - Seeing inside
Download at http://wwwimages.adobe.com/www.adobe.com/products/photoshop/photoshopextended/science/pdfs/ericwexler_fnl_04242007.pdf

4) Photoshop Testimonial Video
View at
http://www.adobe.com/products/photoshop/photoshopextended/medical/

5) White Paper - Photoshop: The Standard for Physicians and Biomedical Imaging Professionals
Download at
http://wwwimages.adobe.com/www.adobe.com/products/photoshop/photoshopextended/medical/pdfs/ps_biomed_wp.pdf

6) Photoshop World Boston – Birds of a Feather - Use of Photoshop Extended in Science and Medicine, April 4, 2007
Birds of a Feather Meeting – Medical & Scientific Research Professionals 
April 4, 5:00 – 7:00 pm 

Hosted by Adobe – Open to Conference Attendees and Medical Professionals and Research Professionals 
Attend this session to see the newest features in Photoshop CS3 and Photoshop CS3 Extended developed specifically for customers who use Photoshop for image analysis, visualization and communication. You'll get to meet the team from Adobe that is charged with developing new features for the medical and research communities and hear from some leading customers in the field and how they use Photoshop in their work.

 Attendees will be eligible to win Photoshop CS3 plus other great prizes.

 Special Guests: Stephen R. Snow, DDS - with Snow Dental Care & Cosmetic Dentistry; Eric Wexler, MBA - Research Scientist with Bristol-Myers Squibb Medical Imaging; Joseph M. Bailey, MD - Montgomery Radiology Associates; and Robert Hurt – Visualization Scientist – Spitzer Science Center.
Track: Special Event — Room: 207 in the Convention Center


7) Photoshop World Las Vegas Workshop
a)Contributed Workbook Chapter - Using Photoshop Extended in Science & Research
b)Conducted Workshop -Using Photoshop Extended in Science & Research
with Eric Wexler 10:45a-11:45a September 6, 2007
Eric will demonstrate the uses of Photoshop Extended in the areas of Biology/Microscopy. He will get into the details on measurement, image analysis, as well as image correction/enhancement for presentations and publications. Additionally, Eric will go over the do's and don'ts of image manipulation for medicine: Instructor: Eric Wexler 
Track: Photoshop® CS3 Extended - Special Interest Track

8) Created Adobe Marketing Material – Adobe Photoshop CS3 Extended for Medical Research
Handout presenting top features of Photoshop CS3 for Biomedical Research

9) Magazine Article – New Analysis Tools
Photoshop User - June 2007 Photoshop CS3 Supplement, pp044-046.

10) Magazine Article – Photoshop CS3 Extended Tools Will Help Save Lives Photoshop User – September 2007, pp074-075

11) Poster – MMP-Activated Pro-Drugs for Imaging Vulnerable Atherosclerotic Plaque. Identification of High Activity MMP Substrates and a Potential Metabolic Trapping Mechanism
Poster Coauthor at Joint Molecular Imaging Conference, Providence, Rhode Island, 2007

MMP-Activated Pro-Drugs for Imaging Vulnerable Atherosclerotic Plaque. Identification of High Activity MMP Substrates and a Potential Metabolic Trapping Mechanism
Category: Imaging in Cardiovascular Disease
Presentation Time: Thursday, 6:30 p.m. - 7:30 p.m.
Thomas Harris, Richard Cesati, Carol Hu, Gregory Dwyer, Reinaldo Jones, Michael Azure, Roushan Afroze, Fran Su, Padmaja Yalamanchili, David Onthank, Eric Wexler, Debra Sousa, Mania Kavosi, Megan Hayes, Paula Silva, David Casebier, Simon Robinson, Scott Edwards, Jeremy Kintigh, Anila Desai, Bristol-Myers Squibb Medical Imaging, Billerica, USA. Contact e-mail: thomas.d.harris@bms.com
Presentation Number: 424
Poster Board Number: 230
Coronary plaque rupture is responsible for the majority of fatal acute myocardial infarctions. Current, noninvasive imaging techniques that assess luminal narrowing or calcium content of plaque are poor predictors of plaque vulnerability. Matrix metalloproteinases (MMPs) are upregulated in vulnerable atherosclerotic plaque and recent studies suggest a correlation between the levels of MMPs and plaque vulnerability (J. Clinical Investigation 1994, 94, 2493-503; Circulation 1999, 99, 2503-9; Circulation 2001, 104, 1899-1904). While radiolabeled MMP inhibitors have been evaluated as plaque imaging agents in preclinical models (Circulation, 2004, 109, 107-112), our own results suggest that MMP levels in plaque deposits from human coronary arteries are too low to provide reliable data using radiolabeled MMP inhibitors.
We present here the initial results of our efforts to develop MMP-activated pro-drugs for the imaging of tissues having elevated levels of MMPs. The pro-drugs consist of MMP substrate peptides, a reporter group, and an immobilizing moiety (hydrazide) designed to react with oxidized lipoproteins found in vulnerable plaque. We have identified a number of substrate-reporter conjugates that have high blood stability, low protein binding, and are cleaved efficiently by MMP-2 and MMP-9 (Kcat/Km = 100,000 to 500,000 M-1s-1). Additional digestion by aminopeptidase N generates the hydrazide. Ex vivo studies have shown that 60% of MMP substrate RP806 is cleaved after incubation with rabbit plaque for 15 min at 37 °C. MMP inhibitors block the degradation and uptake of RP806 in rabbit plaque. Bestatin, an inhibitor of aminopeptidase N, also inhibits the binding of RP806 to rabbit plaque. Additionally, in vivo experiments in ApoE mice display preferential uptake of these conjugates in atherosclerotic plaque. This enzymatic amplification of signal has the potential to detect lower levels of MMPs than radiolabeled MMP inhibitors. Details of the synthesis and biological study of these agents will be presented.

12) Magazine Article – Measuring Using More than Just Pixels
Photoshop User – October/November 2007, pp086-087

13) Research Paper – - Mechanism of uptake and retention of 18F BMS-747158-02 in cardiomyocytes: A novel PET myocardial imaging agent
Padmaja Yalamanchili, PhD; Eric Wexler, MBA; Megan Hayes, MS; Ming Yu, MD, PhD; Jody Bozek, BS; Mikhail Kagan, BS; Heike S. Radeke, PhD; Michael Azure, PhD; Ajay Purohit, PhD; David S. Casebier, PhD; Simon P. Robinson, PhD , Journal of Nuclear Cardiology ,Volume 14, Number 6: 782-8 November/December 2007

Abstract
Background: BMS-747158-02, is a novel 18F labeled pyridazinone derivative designed for cardiac imaging. The uptake and retention mechanism of 18F BMS-747158-02 in cardiac myocytes was studied in vitro and the biodistribution of 18F BMS-747158-02 was studied in vivo in mice.
Methods and results: 19F BMS-747158-01 inhibited mitochondrial complex I (MC-1) in bovine heart sub-mitochondrial particles with an IC50 of 16.6±3 nM that was comparable to the reference inhibitors of MC-1, rotenone, pyridaben and deguelin (IC50 = 18.2±6.7 nM, 19.8±2.6 nM and 23.1±1.5 nM respectively). 18F BMS-747158-02 had high uptake in monolayers of neonatal rat cardiomyocytes (10.3±0.7 % of incubated drug at 60 minutes) that was inhibited by 200 nM of rotenone (91±2%) and deguelin (89±3%). In contrast an inactive pyridaben analog P 070 (IC50 value of >4 µM in the MC-1 assay) did not inhibit the binding of 18F BMS-747158-02 in cardiomyocytes. Uptake and washout kinetics for 18F BMS-747158-02 in rat cardiomyocytes indicated that the time to half maximal (t½) uptake was very rapid (approximately 35 seconds) and washout t1/2 for efflux of 18F BMS-747158-02 was >120 minutes. In vivo biodistribution studies in mice showed that 18F BMS-747158-02 had sustained myocardial uptake for 60 minutes and the heart to lung and heart to liver ratios were 14.1±2.5 and 8.3±0.5 at 60 minutes.
Conclusion: 18F BMS-747158-02 is a novel PET cardiac tracer targeting the mitochondrial complex I in cardiomyocytes with rapid uptake and slow washout. These characteristics allow fast and sustained accumulation in the heart.


14) Magazine Article – A Healthy File Format – Photoshop CS3 Extended Supports DICOM
Photoshop User - January/February 2008 pp82-83

15) White Paper - Optimum Strategies for Using Adobe Photoshop CS3 Extended in Biomedical Imaging – Written for Peachpit on behalf of Adobe

16) Contributor to Presentation – SNAP 2007 Meeting - BMS753951: A Novel Low Molecular Weight Magnetic Resonance Contrast Agent Selective For Arterial Wall Imaging

David Onthank, Padmaja Yalamanchili, Richard Cesati, Joel Lazewatsky, Michael Azure, Megan Hayes, Mania Kavosi, Kelly Spencer, Debby Sousa, Eric Wexler, Melanie Lamoy, Thomas Harris, Carol Hu, Reinaldo Jones, Greg Dwyer, David Casebier, Simon Robinson, BMS Medical Imaging, North Billerica,

17) Training Titles for Lynda.com, Dec 2007, currently undergoing editing
1) Using Photoshop CS3 Extended in Biomedical Research (Working title)
2) Photoshop CS3 Extended Biomedical Workflow Examples (Working title)
Will be accessible online at Lynda.com first quarter 2008, possibly on DVD afterwards

In Progress

18) Website – www.ericwexler.com

19) Blog – ericwexler.blogspot.com

20) Book – Use of Photoshop in Biological Research

21) In person workshops – Photoshop for Biological Research – Starts 2008

Wednesday, November 28, 2007

Drobo - The answer to our storage needs?

Drobo may be the next big thing in file storage.

As a research scientist I have seen my data storage requirements grow and I have been constantly looking for a product that can grow with my needs.

Most recently I have relied on large single disk hard drives as my main storage but with the introduction of data robotics Drobo I am considering that as a viable replacement to my stack of 500GB Lacie drives.

I am not one with enough experience or patience to set up a server or raid device. So when I saw the Data Robotics booth at Photoshop World Boston in 2007 I thought this may be an answer to my prayers directed at the data storage gods.

I was intrigued by three factors. The first is the ability to protect data on the fly using multiple drives in a single piece of hardware without raid configuration. The second is the expansion capability to add drives so the system can grow as hard drive prices decreases and storage needs increase. And third the relative low cost of a unit, inexpensive enough for easy acquisition for lab and personal use.

After multiple encounters with Data Robotics booth staff and explaining to them about the unique needs of Biomedical professionals they sent me an evaluation unit to test out.

I received it about two weeks ago and have used it intensely over that time in the storage of images and other media files as well as backing up my primary production system, an Intel Mac Book Pro.




This is the current picture of the Drobo in use.


Once the box from Data Robotics’ arrived. The unpacking went as expected and I was ready to add SATA hard drives to the unit.

The cover is held in place with a magnetic latch and can easily be removed. Adding the drives was the easiest installation I have seen. The drives slide in ands snap into unseen receptacles fitting power and cables automatically. There are four open drive bays that accept full and half height drives.



Half height 120GB drive in bottom bay.

I won’t bore you with all the details. The rest of the set up went smoothly following the included instructions. I installed the Drobo Dashboard to initialize the Drobo and gain control over options. The Dashboard allows visualization of the status of the unit beyond the informative lights on the front of the Drobo.

The most important factors of any storage device is the ability to hold precious data, “my precious, precious.’

In this regard the Drobo is doing wonderfully. Currently I have approx 650GB of usable data storage with three drives 750, 400, and 320GB. This unbalanced drive size has left 320GB of space reserved for expansion. The kind way to telling that there is some usable space. Using the Drobolator, at www.drobo.com/drobolator, it is easy to configure and optimize drive sizes for the maximum amount of protected storage


Current drive set up in the Drobo and the overall memory situation.

Using the Drobolator I determined that to expand my storage capacity my best next drive purchase should be a 750GB drive (currently ~$180).




Drobolator with optimized hard drive configuration.

My next step will be putting the Drobo through its paces, developing workflows to use the increased storage capacity and confidence in its data protection abilities.

So far it seems to fulfill my in data storage needs. Now lets see how it adds value to my work.

Pros:
1) Provides data protection without the need of Raid configuration
2) Can use SATA drives already on hand
3) Can add additional drives at any time
4) Simple to set up and use
5) I’m am better able to sleep

Improvement Considerations:
1) Correct storage space reported on the Macintosh (Info displays 2TB with Mac operation system)
2) Higher speed transfer (The current Drobo uses USB 2.0 port, why not add additional options)
3) On/off switch ( The unit powers down when the computer is turned off but sometimes I may just want to have the unit off without unplugging the power


Data Robotics Drobo Storage Robot Multiple 4-Drive Enclosure ~ $480 online