SpotReader produces grids for printed (or "spotted") microarrays. It then uses these grids to analyze the images and produces tables of statistics about each microarray.
Other programs do this, so what's new about SpotReader?
Truly Automated, Walk-Away Gridding and Image Analysis
SpotReader is the first microarray program that can honestly boast truly automatic gridding. It requires only four simple parameters describing the number of rows and columns of blocks and spots. It then automatically produces the entire grid while you watch, and with its batch processing, it can produce dozens of grids while you take a coffee break.
You don't need to tell SpotReader where to start, nor do you need to enter column spacing, rotation, feature diameter, or draw lines or even set block positions. Blocks down and across, spots down and across; four numbers, that's it!
It's so ridiculously simple that some people don't believe it's possible. When you are done with this overview, please take a moment to watch our Quick Overview video and see for yourself.
SpotReader works on dim arrays, packed arrays, smeared arrays, misaligned arrays, and even arrays with bowed columns or rows!
SpotReader works. It's that simple.
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Real-Time, Seamless Updating
SpotReader is real-time...and VERY FAST! When you make changes, the images, the analysis results, the scatter plots, everything is updated automatically. No longer do you have to figure out how to move from one mode to another ...or then have to wait and wonder if the data have been updated. SpotReader does it all seamlessly and thus keeps everything up-to-date.
Move a feature - the flagging and analysis results automatically update. Change a flagging parameter - the images and results update as you watch. Edit a feature while viewing analysis results - the flagging and results automatically update.
It's seamless and it's FAST!
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The Industry's Best Viewing and Editing Tools
Although the grids automatically created by SpotReader will frequently be refined enough to use unedited, we provided many powerful tools to allow you to easily view the resulting grids and to make minor changes that you might feel necessary.
Using a state-of-the-art, familiar Windows interface with modern menus and docking toolbars, SpotReader allows you to view, modify, and analyze your data with unprecedented ease.
Features can be moved and resized with the mouse or with keyboard shortcut keys. SpotReader does away with confusing edit modes and allows you to edit blocks and features within a single mode; simply click on their borders and make any change you desire. Editing a grid has never been so easy.
SpotReader draws a dotted line around the outside of features, but when zoomed in, it also shows you a lined border around the outside of the spot so you always know exactly which pixels are included in the feature. While most programs only show circles (and some even treat odd and even diameters as the same size!), SpotReader's edged ellipses show you exactly how each feature is defined. This makes it science, not magic!
SpotReader has 100 levels of full undo and redo. Everything you do can be un-done including moving features, blocks, flagging, and even auto-aligning!
You can resize a group of features to see how it affects the data, move them again, and again, and again ...and then undo every single step! SpotReader's undo/redo is so sophisticated that you can move the entire grid dozens of times and then undo as much as you want...
and when you're done, you can even redo each and every step! It's amazing!
Of course you can edit the grid in the image window, but because the feature viewers are fully editable as well, you can even edit features while you view the analysis results or look at the scatter plots! Move the cursor over the data table or scatter plot and each feature's images are immediately updated. Sort the results based upon some criterion and then edit the features that concern you all from within the results or scatter plot views! It's that simple.
Say goodbye to clunky, arcane, and out-dated programs and start using SpotReader today!
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Elliptical Features
SpotReader introduces the ability to define features as ellipses or as circles (for backward compatibility).
Ellipses form a much better fit than circles and they avoid the powerful biases that are inherent in threshold-based, irregular-shaped feature locators. In addition, since ellipses fit better, you will manually adjust far fewer features and thus keep data analysis more consistent from array to array.
Put simply, we have found that ellipses (which include circles) fit the real fluorescence signals better, and give you more good data.
After looking at hundreds of arrays from dozens of labs from around the world, we've seen that most arrays include a large number of significantly elliptical spots that simply cannot fit within a circle. Using circles forces you to constantly choose whether to include too much foreground or too much background. With ellipses you can include the entire feature and thus avoid the fundamental inaccuracy of simple circles.
You spend weeks or even months preparing your slides. Your experiment deserves the consistency and robustness of SpotReader's elliptical features.
Use SpotReader and
get more good data today then ever before.
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Automatic, Real-Time Flagging
SpotReader flags bad features automatically based on eleven user-selectable and adjustable criteria. As you modify these parameters, you see the image reflect the changes (and the same is true when you're viewing the analysis results).
SpotReader is real-time so the image is updated continuously as you make changes to the flagging parameters or if you edit a spot. If editing a feature results in changes to neighboring spots, their flags are also updated. Make a change in a flagging parameter and watch the image (or analysis results) reflect the change.
Even if you don't use flags in data analysis, flags can help you visually inspect the grid.
Automatic flagging lends a high degree of objectivity to the data analysis. You don't have to rely on your monitor or your eyes, and your mood or energy level won't affect your results!
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Effortless Batch Processing
Like many of its features, SpotReader's batch processing is very sophisticated, yet optional. Initially you may ignore its capabilities, but in time you will wonder how you did without it. You don't need to use it...but it's so simple, we know you will!
You can define file "associations", that is, very simple naming characteristics that distinguish your different batches of arrays. These associations tell SpotReader how to create grids for any array matching those rules.
For example, you might name one batch of arrays PR202_1, _2, _3, etc. and a second batch AR1073_1, _2, _3, etc. After you define one file association for each batch, SpotReader will know the spot layout for all files that begin with PR202 and AR1073. You only enter the number of rows and columns of blocks and features once - then, anytime SpotReader opens images matching the associations, it knows exactly how to process them!
You can even define a "watch" folder where SpotReader will periodically look to find arrays that it then automatically grids and analyzes. Drop the images from your scanner or core facility into the watch folder and SpotReader will find them and automatically output the results. And if you're not quick enough, SpotReader will finish before you even have a chance to sit down!
Avoid the tedium and error-prone ways of your past. Use file associations so you need enter parameters only once for all the arrays in your print run.
SpotReader works hard so you don't have to.
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Mini Database That Automatically Remembers Every Array
SpotReader uses a mini-database to automatically keep track of every array it loads. This database gives you easy, one-click access to each array and the images and grid associated with it. You don't have to do anything. When SpotReader sees a new array being loaded, it adds it to the database. When it recognizes a file has already been loaded, it automatically shows you the related files and offers to open them all at once.
Use the database to open an array simply by double-clicking on it: the images and grid automatically open together. No more finding and selecting multiple files, the database does it all for you.
(SpotReader's Open File dialog also has intelligence: select an image or grid and SpotReader will show you its matching images/grids...even if they aren't in the database!)
Drag-and-drop a group of images onto the database window and it will automatically add them to the database...and if you've defined file associations for them, it immediately begins gridding each without requiring any input from you!
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Next Generation User-Interface
SpotReader is fully customizable. The novice need not change anything and the expert can configure it to their delight.
Windows can be moved and resized. Toolbars can be docked or floated. The feature viewers (zoomed-in images of each separate image showing individual spot under the cursor) can even be resized! You can add commands to the toolbars and change keyboard shortcuts. You can even have toolbars and the Feature Information and Flagging dialogs automatically hide and show themselves by docking them to the sides of the window.
SpotReader is indeed fully customizable...but we doubt you will modify much. We've worked very hard to put windows and toolbars in reasonable default locations and we chose shortcut keys to ease learning and to allow the left hand to be on the keyboard and the right to be on the mouse.
We've sweated the details so you don't have to.
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Details, Details, Details
When you use SpotReader you will notice the attention we paid to the details. When we built each tool, we worked very hard to address your needs and worked even harder to hide much of the underlying complexity.
Without a doubt, SpotReader's simplicity is one of its greatest features. Or is it its flexibility?
For the novice user, we've made all the important features extremely easy to use. For the expert users, we've provided the tools and a user-modifiable interface to allow SpotReader to work the way you want it to.
Other details include:
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Almost every menu item has a shortcut keyboard command and we've even included an item in the Array menu that pops out a list of other shortcut keys.
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A pop-up magnifying glass that allows you to zoom in on an area of the image with the press of a key!
- A pin-mode that allows you to move entire sections within a block with only two mouse clicks.
- Fast, fast image updating. When you edit a feature or move a block, you see results immediately.
- Reads files from other applications including GenePix® and Scanalyze.
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You will love what you see: we guarantee it!
Be sure to watch the Quick Overview video for a brief introduction to some of the features discussed above.
What is a "Grid"?
SpotReader creates and uses a grid as the means to identify the spots, and to differentiate between the foreground and background of each spot on an array. An array is made up of one or more images that are each the output from a microarray scanned at separate wavelengths. An array is usually divided into rows and columns of blocks, which in turn are aligned in rows and columns of spots. A spot is a single pool of reagent that appears as a round or elliptically bright area in the images.
A grid, then, is an arrangement of circles or ellipses overlying the image. Each circle or ellipse is called a feature, and the features are arranged in rows and columns within a block. The pixels falling inside the circle or ellipse are the foreground pixels for that feature, and the pixels falling outside any feature are the background pixels (although pixels near the outside border of the features are usually ignored during analysis).
The rows and columns of each block may be aligned in a rectangular or orange-packed format. The former is where each row is aligned to the row above and each column is aligned to the column to the left. Orange-packing is where every other row or column is staggered, or indented, relative to the row or column above or to its left.
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