The first of the new REDFIN manuals available now!

New and interactive technologies are great, no question about that.

But lets admit it, sometimes it is nice to be able to print something out and read it the good old fashioned way. To touch the paper, scribble notes on the side and highlight the important passages.

That’s why we decided to create some good old printer friendly manuals for REDFIN in addition to the other more interactive support material we provide.

To make it easier to find the relevant sections, we have split them up into distinct chapters, which are listed on the manuals page on our website.

Also, within each chapter there are sub-categories that allow you to jump right to the part you are looking for.

And just because we’re creating some nice printer-friendly, old-school manuals doesn’t mean we’re going to churn out an incomprehensible, bore-you-to-tears novel… no mister! We want you to have the same mind-blowing, awesome experience with our manuals that you have with our software products!

Well, ok, that might be asking for a little too much, but hey, we’ll do our best to make them as enjoyable as manuals can get.

So without further ado, we present to you the first chapters of the REDFIN manual:

Just click on the image below to jump right over to the list of chapters.

More chapters are being written as we speak and will be added to this page shortly. We’re also planning on creating one big PDF document that contains all the separate chapters in one handy document.

So sit tight, good things are coming your way…

Filed under: News

How to export your 2D gel data from REDFIN: Excel export

REDFIN basically offers you four ways of exporting your 2D gel image analysis results.

1. Exporting for picking

2. Exporting to a PDF report

3. Exporting to an Excel spreadsheet

4. Exporting the raw data

In this post we will focus on options 3 and 4, which are probably most attractive to you if you are intending to process the data further. This may include creating more elaborate, user-defined graphs, applying custom-made algorithms, or running more specific statistical analyses.

Depending on if you would like to export all spot volumes in the project or only selected spot data, you should choose between the export option on the start page (exporting the raw data), or the Export To Excel option in the results view.

Let’s look at those two in more detail.

Exporting the raw data

On your REDFIN start page you will see several different project specific actions listed on the right side of every analyzed project. One of these actions is “Export” and indicated by a white arrow in a orange circle.

The red box marks the location of the Export button on the REDFIN start page

For any project that you wish to export the analysis results for you simply click this button and choose if you want to export the data with or without images. A compressed .zip file will be saved to your computer.

When extracting the files you will find one spreadsheet named RawSpotData. This file contains all spot data, including position, border, and normalized volume for each spot in each gel.

In addition, there is a file called SpotVolumeMatrix. This contains only the normalized volumes – arranged in a grid versus each protein ID. This file is more suitable for quick plotting and comparing of volumes for each protein.

If you ran a DIGE experiment, these files will also contain the spot volumes of the cy2 internal standards.

Exporting to Excel from within the Results View

In most 2D gel image analysis workflows you will not want to export the entire data set after you are done finding proteins of interest. Instead, you will probably want to export only those protein ID’s that you deemed significant in one way or another.

The export to Excel option in the Results View will allow you to do just that.

After selecting the comparison you are interested in, filter the list until only proteins of interest are left (although you can of course export the entire list without filtering, if you would want that).

Just underneath the first comparison tab you will see how many spot ID’s are left in the list after filtering.

Remember that if you have star rated spots, you need to make sure to also filter on the star property in order to only export the star rated spots.

When you are ready to export the contents of the list simply click on the little Excel icon located in the top right of the screen.

After choosing where you would like to save the generated file, REDFIN will automatically start exporting all the values that are currently present in the list to an Excel spreadsheet.

The spreadsheet is already pre-formatted, and not only contains general information about the experiment, such as experiment name, comparison, groups, and filter settings used, but also statistics and individual spot normalized spot volumes.

Remember, that the main difference between exporting from that REDFIN start page and exporting from the REDFIN results view, is that exporting from the start page provides you with all the spot volumes from all the gel images in the project, whereas exporting from within the results only focuses on the spot volumes of a (probably) filtered list within a selected comparison.

If you are unsure about anything, don’t hesitate to contact us directly at support@ludesi.com.

Filed under: How to's in REDFIN , export data to excel

New Feature in REDFIN: Easy Image Inverting

Does the following image look familiar to you?

Sometimes image capture of your 2D gels results in an image with inverted spot intensities.

Although REDFIN is able to handle inverted 2D gel images, some of you wanted the ability to invert those images before proceeding down the analysis workflow chain.

As we recently added image editing functionality into REDFIN, it was pretty straightforward for us to also add a tool for inverting your images.

Now when you enter the REDFIN analysis workflow you will see a button on the edit image step that does just that.

As always, the image manipulation carried out in REDFIN is for visual purposes only and will not alter the image itself, thus not affecting the actual analysis.

Make sure to keep the feedback coming (the good and the bad) so that we can continue creating tools that are just perfect for the job at hand.

Filed under: New features in REDFIN , Image editing

Visiting the HUPO 8th Annual World Congress in Toronto

Last week we greatly enjoyed taking part at the HUPO meeting in Toronto.  For those of you unfamiliar with the Human Proteome Organisation (HUPO), it can be described in a nutshell as aiming to foster international proteomic initiatives to better understand human disease.

Since it’s launch February 2001, HUPO has been organizing world congresses every year and lucky for us at Ludesi, this means we get to jet-set to exciting cities such as Seoul and Amsterdam, and meet some of the leading researchers in the field. As always, we greatly enjoyed meeting old as well as new faces and hearing about whats new and what’s hot in the world of proteomics.

Probably as a result of the financial crisis, this years meeting in Toronto was slightly smaller than usual, but still well enough attended to ensure you will never be able to meet and see everyone/everything you would like to.

The talks and posters provided us with a great overview of the cutting-edge science currently being carried out in proteomics and taken together with the stimulating discussions we had, we have returned to Sweden with lots of great ideas for REDFIN and Ludesi in general.

Unfortunately, the organizers failed to schedule specific poster sessions this year, which meant it was difficult for the presenters of posters to interact with those interested to discuss their research further. Lets hope this gets rectified in next years HUPO taking place in wonderful Sidney!

G’day mate! Looking forward to being there!

Otherwise we’d like to thank everyone involved for making it such an enjoyable event!

Filed under: News, Random Ramblings

New look for the Ludesi website!

To keep up with all the new developments and products created in the last few years, the Ludesi website has been completely revamped and given a fresher look and feel.

In addition to applying a new lick of paint, we wanted to improve the organization on the website, in particular how easy it is to access resources and support material surrounding the REDFIN software.

Now, everything to do with the REDFIN software is grouped together under “Software”, whereas all image analysis service pages can be found under “Services” (no surprises there!). Most importantly, we’ve pulled together all support related material and given it it’s designated section called “Resources”.

For those of you who prefer to have printable support material, we have reserved a space under “Resources” that will contain REDFIN user manuals in PDF format. But be patient – we know they’re not up there yet, but if you check back in a week or two you should find them up and accessible…

Finally, it’s also worth to point out that we have installed a site-wide search functionality that will pull out any relevant material to your keywords. That way it should be even quicker to find what you are looking for.

All in all, we are extremely pleased with our new site and hope it will make browsing all Ludesi-related material even more enjoyable and easy for you!

Visit the Ludesi website

Filed under: News

10 days left for free 2D gel image analysis in REDFIN Solo: what happens afterwards?

All good things must come to an end they say and unfortunately this is also the case for the REDFIN Solo summer campaign.

If you are one of the many scientists who have been using the REDFIN Solo 2D gel image analysis software for free, you may be wondering how the end of the summer campaign will affect you.

Accessing your existing analysis projects after September 30:

Any 2D gel image analysis data that you have created during during the REDFIN Solo summer campaign will continue to remain freely accessible to you.

• You will be able to log in to your REDFIN account as usual and open any projects by clicking on the project name on the start page.
• All features in the REDFIN software for working with your results will continue to remain available to you at no cost.
• All your data will continue to be securely backed up at our servers at no cost.

In short, nothing will change for existing projects in your account.

Analyzing new 2D gel images after September 30:

Any new analysis projects will have to be paid for by purchasing image analysis credits directly in the software.

• To pay for the analysis you simply buy one credit per 2D gel
• One credit costs 30 USD or 21 EUR
• You can watch this 2 minute video on how to pay in REDFIN Solo

Remember, you will be able to preview your results before deciding if it is worth purchasing analysis credits for them, according to our “pay only if you’re happy” principle.

If you have any questions, don’t hesitate to get in touch with us at support@ludesi.com.

Filed under: News , Free Redfin software

Last month for free 2D gel image analysis!

“There’s no such thing as a free lunch!” they say, but I guess at Ludesi we have a tradition of doing things differently…

When we launched REDFIN Solo 2 months ago we knew it was something special. There is no other 2D gel image analysis software on the market that combines state-of-the-art algorithms, a workflow driven user interface for an easy and fast analysis, with an affordbable pay-per-gel system.

And those are just the basics…

In addition, the software offers some real innovative goodies:

• Install as many copies of the software on as many computers as you like
• Pay only for results that look good to you
• Share your projects with whoever you want (and we’re talking proper sharing – not some emailing of static PDF reports…)
• Work together on the same project from different locations
• Have your data automatically backed up every 30 seconds or so…
• If you run short on time, simply request a professional analysis service directly within the software

Still, we knew that despite it being a real gem on the 2D gel software market, we needed to give REDFIN Solo the chance to really get known and loved by the proteomics community…

And what better way to do that then letting people really try it out for themselves – extensively – on their own data?

Enter the free REDFIN Solo summer campaign!

Since starting the campaign beginning of July lots of scientists have downloaded REDFIN for free and hundreds of 2D gel projects have been analyzed at no cost at all.

As people have been using the software, we’ve also received some great feedback, which has led to the incorporation of the “Rotate and Flip Images Tool” and the “Merge and Split Spot Borders Tool” into REDFIN. Again, at no additional cost to our users.

Now, we are two thirds through the campaign and still there are new people downloading REDFIN every day.

If you haven’t tried REDFIN Solo for yourself there is still one month left to do so without paying anything. And if you don’t have any 2D gel images to analyze right now, don’t worry – at only $30 per gel it will hardly break the bank to test the software after the campaign ends…

Filed under: News , Free Redfin software

New Feature: Split and Merge Spot Borders

It seems that despite the hot summer weeks productivity at Ludesi has if anything increased, with one new feature or improvement being churned out after another.

This time we have implemented something that we know you have been wanting for a while: merging and splitting spot borders.

Before we dive into describing these new tools to you, here’s a quick overview of what editing possiblities you have in REDFIN today:

As usual, you access these tools by opening your results in REDFIN and clicking on the “Edit Spots” button in the Spot View.

But now, let us introduce you to the final two tools in the spot editing toolbox:

1. Split Border

Whenever you see a spot border that encompasses more than one spot, this is the tool to go for. In the spot editing mode, select “Split border” from the menu on the right and you will see that your cursor changes to a little knife. Now all you need to do is to draw a line where you would like to cut the border in two.

Release the mouse and the spot borders will split exactly along the line you have drawn.

If you are not happy with the split, just click “Undo” and try again.

2. Merge Borders

Sometimes the spot detection has been too sensitive and two or more spot centers have been detected where really there is only one. With the Merge Borders tool you can easily combine neighbouring spot borders into one border. All you have to do is draw a line showing which spot borders you would like to connect.

Release the mouse and the two neighbouring borders are combined into one spot border.

As with all editing tools, if you regret your last action, click “Undo” to reset the previous state.

We hope you enjoy the new tools and that they will make working with your results in REDFIN even easier!

As always, we welcome any feedback you have for us.

Filed under: How to's in REDFIN, New features in REDFIN , Spot editing

New Feature: Rotate And Flip Images Directly In The REDFIN Software

You asked for it and now it is part of the REDFIN workflow: an easy image manipulation tool that allows you to rotate and flip your images.

Although there are many free image manipulation tools out there, we felt it was important to incorporate this directly into REDFIN. After all, we generally don’t recommend you to manipulate your 2D gel image files using third party software, such as Photoshop, as it is surprisingly easy to lose information from the file on the way…

The flip/rotate tool in REDFIN will of course protect your images from such a thing happening and will keep the original file intact. The tool will be presented to you as a second step in the setup workflow, right after uploading your image files.

Go through all the images in the project using the image selector box on the right side to check if any images need manipulating.

The Rotate Tool lets you rotate your images both to the left and to the right.

The Flip Tool lets you flip the images both horizontally and vertically.

You should now be able to quickly and safely adjust all images to ensure that they all have the same orientation in the project.

If you can think of other features that you feel would make REDFIN an even better tool for you, make sure to let us know! You can do so either by commenting on this post or contacting us directly at support@ludesi.com.

Filed under: New features in REDFIN , Product Update

How to add or remove gel images from an existing analysis

Here is a common scenario:

You analyze your 2D gel project, and start working with the results only to realize that you would actually like to change the comparison you have previously specified. Maybe there is a gel that didn’t run very well and is messing up your statistics? Or maybe your initial investigation has inspired you to create sub-groups and get the statistics on those? Is there a way that you can easily do that without re-analyzing the entire project?

The good news is that there is a very easy and fast way to do this in REDFIN.

Step 1: Open up an already analyzed project in REDFIN.

Step 2: Click on the “Manage comparisons” button in the top right corner of the screen

Step 3: Select the comparison you wish to edit or create a completely new comparison if you wish to keep the results of the existing analysis

Step 4: Select the group you wish to change or create a completely new group.

Step 5: Add or remove any images to the group by double clicking on it or by simply dragging and dropping it into the bottom image container.

Step 6: After you have made the required changes click on the “Back to results” button. All statistics are re-calculated on the fly.

With the Manage Comparison functionality you have the freedom to change and add comparisons as much as you wish, even after completing the initial analysis of your gels.

All comparisons you create are shown as different tabs enabling you to easily skip between them. The REDFIN results interface links all spot ID’s together, so that if you select one spot by clicking on it in the list, and you then click on a different comparison tab, the same spot ID is automatically shown. This allows you to quickly compare statistics on the same protein spot between different comparisons.

Filed under: How to's in REDFIN, Tips and Tricks , comparisons, statistics