SameSpots

 

"The alignment procedure in SameSpots allows truly near complete matching of all spots across all the images of the experiment. And this is done in a fast, nearly automatic way. This makes not only image analysis much easier, and operator independent, but it makes statistics much more robust. Using  SameSpots to analyze 2D-gel experiments, you feel much more confident that  you are getting the most information out of the data. No worries about differences not detected as significant because of poor matching, ... without spending hours and hours reviewing the results. The built-in statistics provide also nice tools to check the consistency of the data through PCA analysis, find patterns of expression, and evaluate the significance of observed differences. By adding up simplicity of use and strong results, SameSpots has gone really close to what one would have dreamed of  2D image analysis software some years ago."

Francesc Canals, Institut de Recerca Hospital Univ. Vall d'Hebron, Barcelona

"Since we got the program a lot more people are doing 2D"

Dr. Metodi Metodieb, University of Essex

“Nonlinear Dynamics has identified the problematic issues associated with 2D analysis and solved them elegantly with SameSpots. 2D analysis is no longer a chore, more of a pleasure.”

Dr. Steven Banner. Neuropathogenesis Unit, Roslin Institute

“I am very happy with the software - I started with Phoretix 2D several years ago at Dartmouth College, and every time I use a new version I am impressed. It seems the programmers are really listening to what's needed by the users and are incorporating those features.”

Dr. Naomi Etheridge, University of Queensland, Australia

“SameSpots is the smart way for the 2D gel image analysis. No more subjectivity and iterative spot edition in the matching process. More importantly, the analysis is fast and straightforward thanks to the intelligent workflow, from image quality checking to gel alignment, to spot selection and edition and final results. In addition, the powerful statistic tools help to objectively decide in differential expression experiments.”

Roque Bru-Martinez, Proteomics Facility, Universidad de Alicante, Spain

“The results obtained with Progenesis SameSpots are comparable to our current analysis package and took significantly less time to process. This has confirmed my view that SameSpots is superior to our current analysis package in terms of speed with the added advantage of a user friendly interface and statistical tools.”

Dr. Mark Weeks, Ludwig Institute for Cancer Research, UCL, London

"Progenesis SameSpots is by far the best 2D gel quantification software I have ever used. It provides great improvement in speed and I like best its intuitive workflow. It brings my analyses to a new level of accuracy."

Dr. Reto Portman, Friedrich Miescher Institut (FMI) for Biomedical Research, Switzerland

“Using SameSpots, I have managed to get more out of my data in the last week than I have done in the last 2 or 3 years”

Phillip Cash PhD, Department of Medical Microbiology, University of Aberdeen

“We have enjoyed using SameSpots because it combines fast visual analysis, exceptionally reliable alignment and spot matching and quantitation as well. And it allows us to quickly focus the spots showing interesting expression patterns.”

Dr. Anna Chiarini, University of Verona

"We have a lot of experience analysing 2D Gels; we started using image analysis software in the mid-eighties. Since that time, we got almost everything available on the market. Progenesis is up to now the only software that gives us the full flexibility we need to analyse our gels. Now, I believe that by aligning the gels prior to the detection using TT900 S2S and then applying the SameSpots approach in Progenesis, I will be able to dramatically reduce my hands on time and further increase the level of confidence in my results."

Dr. Delphine Vincent, INRA, Ferme du Moulon, Proteomics Platform, France (collaborator of Michel Zivy

"TT900 S2S represents a quantum jump in 2D gel image analysis. Using an appropriate statistical toolbox, we have seen a real improvement in overall data quality, with the supplementary time and resource savings that this will result in. As such, we have added the TT900 S2S to our standard 2D gel analysis methodology"

Jan van Oostrum and Hans Voshol - Novartis Institutes for BioMedical Research

“SameSpots is much advanced and ahead of its competitors. It has reduced the analysis time to minutes from hours. Its statistical power is unmatched; with the ability to find same spot on all of the gels on exactly same location, problem of missing values from the gels is gone. SameSpots is definitely better than previous versions and is much advanced than its competitors.”

Ashutosh Gupta, student of Prof. Ramon Gonzalez, Rice University

“Progenesis SameSpots represents a superlative software package to tackle 2D gel image analysis by means of an intuitive and unbiased workflow. The efficiency of gel warping and spot matching has greatly reduced the bottle necks in image pre-analysis processing. We have used SameSpots to analyse DIGE images of plasma and joint fluid from juvenile arthritis patients. The software allows us to quickly focus on those proteins which are sentinels of systemic or localised inflammation. With SameSpots we are able to highlight significant changes between patient subgroups with a higher degree of confidence, as previously overlooked missing values are now retained within the data set.”

David S. Gibson, PhD Research Fellow Arthritis Research Group Queen's University Belfast Musculoskeletal Education and Research Unit

"The statistical analysis of quantitative protein expression data from 2-DE proteomic experiments has previously been compromised by extensive "missing" data, due to problems of spot detection and matching between 2-D gels within an experiment. This problem has been completely overcome with the advent of Progenesis SameSpots, allowing us to apply more rigorous statistical tests. SameSpots provides much faster analysis of large 2-D gel data sets because of the reduced need for user interaction to carry out tasks such as spot editing and manual matching between gels. The results are therefore more objective and we have much greater confidence in their statistical validity."

Mike Dunn, Professor of Biomedical Proteomics, UCD Conway Institute, Ireland and President of the British Society for Proteome Research.

"By adopting these new image analysis technologies, our rate of discovery using 2D electrophoresis stands to be significantly enhanced. An additional benefit is that this new approach to 2D image analysis can be easily incorporated into our existing workflow"

Professor Steve Pennington of the UCD Conway Institute, Ireland and Vice and President of The British Society of Proteome Research (BSPR)

“Everything about Nonlinear Dynamics makes it a great company to work with. The sales team really knows the product, technical support is excellent and readily available, and the software package itself is superb. The SameSpots upgrade gives an already great software package even greater accuracy. Being able to perfectly line up our gels increases the confidence we have in our results and reduces the chance for false negatives and positives. We would not do 2d gel analysis without it. The whole analysis process is easy, is highly accurate, and provides statistically meaningful results.”

Merry L. Lindsey, Ph.D., Assistant Professor, The University of Texas Health Science Center at San Antonio

"The Mass Spectrometry and Proteomics Facility at Montana State University possess several 2D image analysis software packages. As an open access facility with user experience ranging from undergraduate to faculty level, we have been very pleased with the ease of use of the Progenesis SameSpots software. The image pre-alignment prior to spot detection is truly a step forward in analyzing gels with high batch-to-batch variability such as human depleted serum sample analyses. The intelligent noise correction algorithm and advanced background subtraction algorithms are important in spot evaluation. The inclusion of sophisticated statistical analyses products is a boon in the examination of disease-dependent alterations in human tissues/serum. We strongly feel that the Progenesis SameSpots algorithm is step above other commercially available products."

Dr. Rachel Neal, Mass Spectrometry and Proteomics Facility, Montana State University

“The differences between Progenesis SameSpots and traditional 2D analysis are profound. The old way required extensive spot editing and manually correcting the matching, which took a very long time. With SameSpots, the analysis is much less time-consuming.”

Nancy Kendrick, Ph.D., Kendrick Laboratories

"TT900 S2S incorporating SameSpots delivers an alternative starting point for 2D image analysis - offering significant improvements in image matching. The benefit of reliably matching spots across all gel images from the start means you can quickly focus your research efforts on investigating the few spots showing statistically valid changes, which are indicative of potentially interesting expression profiling changes"

Professor Mark S. Baker, CEO, Australian Proteome Analysis Facility Ltd (APAF)

“Since implementing the SameSpots approach, the changes we have noted in our analysis have been very encouraging. The ability to perfectly align images within the experiment before applying SameSpots detection dramatically improves matching performance. This enables highly consistent and reliable results to be obtained from all our 2D data sets, even those that previous image analysis packages were unable to accurately quantify”

Dr. Peter Ashton, University of York, UK

"TT900 S2S incorporating SameSpots delivers an alternative start point for 2D image analysis which offers significant improvements in matching. The benefit of reliably matching spots in all gel images from the start means you quickly get to the exciting spots that show the real differences"

Dr. Brad Walsh, Minomic Pty Ltd, Australia

“SameSpots is a new way to think about 2D gel analysis. Now you can enhance the sense of your raw images for a more accurate and less time-consuming data mining.”

Jean-Philippe Charrier, BioMerieux, France

“I am a fan of the new SameSpots approach which allows me to easily realign my gels prior to analysis. SameSpots also reduces my hands on time while increasing the quality and the level of confidence in the results produced. I am very excited to be pioneering this technology.”

Dr. Jean Louis Dacheux, INRA Nouzilly, France

“The SameSpots option is simply wonderful and I am so happy because it makes life so much easier for us! Currently we finalise several large 2D projects and spend so much time to find the significant alterations - which will be so much easier from now on. To give you an estimation spot correction based on detection and comparison to a reference gel took about 3-6 hours per gel. Now we only need to align the gel, which takes us about 30-45 min per gel.”

Christopher Gerner, Associate Professor of Medical Biochemistry, Medical University of Vienna

"At PRS a big part of what we do is analyze gels and we know the issues. SameSpots in our workflow has definitely increased our analysis capacity and therefore allows for faster turnaround times for projects. The modest amount of editing required gives us the confidence that the results generated are completely objective"

Mike Pisano, President, Proteomic Research Services, Inc

"The major advantage of the software Progenesis SameSpots is the ease of alignment of the gel images with conservation of the aligned images. We particularly appreciated the efficiency of the team of Nonlinear Dynamics during our first steps with the application."

Drs Catherine Grenot and Françoise Descotes, Centre Hospitalier Lyon Sud, Lyon, France

“I installed SameSpots and the only problem I have with it is that I am getting addicted to working with it! I don't think I could go back to working with any other software”

Cristina-Maria Vâlcu, Forest Genetics, Technical University of Munich

"We used to spend a lot of time in matching gels after spots detection and SameSpots revolutionizes the usual strategy by starting to align gels before. The way they develop saves time and energy with an increase confidence in the results we get, by applying co-detection and noise removal."

Dr Christian Beauvallet - INRA - GPL/GEL

"Before SameSpots the time limiting step in our 2DE work was the image analysis now it is the production of 2D gels. The image alignment prior to spot detection and quantification performs really robust and reproducible. In a 2D data set the spot detection differs depending on which gel is chosen as reference, but due to the 100% matched data and no missing values the final results are very close to the same, independent of the chosen reference gel. This demonstrates a high degree of objectivity in the fast and nearly hands-free image analysis by SameSpots, increasing our confidence in the obtained results."

Dr. Flemming Jessen Danish Institute for Fisheries Research

“We have used 2D analysis software from NLD since the very earliest released versions but with SameSpots we have significantly improved our approach to processing 2D gel data. We can compare 2D gels more efficiently with a high level of confidence in the derived data. The combination of the new warping routines and robust protocols for spot detection across the gel series means that we can now redefine our whole workflow in the use of 2D gels for proteomic research.”

Phillip Cash PhD Department of Medical Microbiology University of Aberdeen

"SameSpots nous a apporte un gain de temps enorme dans le traitement de nos gels. Il est assez intuitif et nous sommes vraiment tres heureux de son acquisition. Le point le plus important pour nous est la fonction "100% matched data " qui assure a mon avis un meilleur traitement des resultats."

Catherine Guette Centre de Lutte contre le Cancer Paul Papin de Angers Laboratoire d'Oncopharmacologie

“Performing alignment before spot detection reduces drastically the analysis time and improves the matching performance. Consequently, the quality of statistical data improves and any significant alterations can be easily calculated. By using completely matched experiments the impartiality of analysis is warranted, giving confidence in results collected.”

Prof Lello Zolla, Universita della Tuscia

Coverwise

“We've always found Nonlinear's support to be quick, responsive, thorough and you guys always follow up to make sure that you've addressed our needs. With software with so many different capabilities, this sort of constant customer service, backup, and advice is invaluable.”

Christina D Shields, Veterinary Science, University of California at Davis, US

“I have never had a problem that Nonlinear Support could not solve with a short phone call or a concise e-mail. They know their stuff and communicate well.”

Ryan Chafin, Vital Probes, Inc, US

“Nonlinear Dynamics after sale support is first-class. It is easy to request help from the Nonlinear support team via the software itself and every response is thorough and expertly explained – not to mention how quick they reply - even if you are from down-under on the other side of the globe! The Coverwise Support resources are an invaluable knowledgebase for using the software and analysing your data powerfully. I am always confident that I can use Nonlinear Dynamics software to achieve my research goals.”

Julie Soon, Australian Proteome Analysis Facility Ltd (APAF)

The technical support we have received has been very good indeed, with questions being answered very fully and quickly. We really have been very impressed by the level of support.

Dr. Rachel Craven, Cancer Research UK Clinical Centre, St James's University Hospital, Leeds, UK