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LEGENDplex
 

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The LEGENDPlex MAC version doesn¡¯t support any dongle. Instead it uses a File license. Please review the Installation Guide and follow the steps to generate license request file (LEGENDplex.lxr). Please email me it lxr file with a lot number of BioLegend assay kit. Then I will be able to generate you a license file.     Simply just try to launch the software, follow the instruction on the screen for generating a license request file.

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It is the Security set up on you MAC blocks you copy lxx file. Here are the steps to reset your computer: At the ¡°System Preferences¡± screen, click ¡°Security & Privacy¡±.

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To resolve your problem, you could try to reset the set up to Default.

At Step 2 of the analysis, click ¡°Load Defaults¡± in the Options dialog box below:

Then continue the analysis.

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MicroVigene
 

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MicroVigene automatically finds the blocks that are at the minimum, 100 pixels apart. MicroVigene also allows you to manually draw rectangles to define blocks, which can be saved in the template. MicroVigene can automatically align grid and locate spots as long as the grid patterns are visible.

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MicroVigene use a flexible-grid approach to correctly locate the skewed grid lines as shown below.

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You can set  the three anchor points (top-left, top-right, and bottom-left) by right clicking the ROI (Region Of Interest that contains a block) object and select "Show Anchor" in the popup menu.  Drag and align the anchor points and then click the GO button again to re-define spots.  

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MicroVigene finds actual spot boundaries instead of just centers of spots.  Finding spot boundaries is much more challenging than just centers of the spots and computational intensive.  The benefits are well worth it and MicroVigene analyzes an image in less than a minute (see the next FAQ).

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With spot boundaries well defined, spots can be more accurately allocated. It can also correctly separate spot pixels from background pixels, which enables you to subtract background correctly. 

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Since human eyes can only see maximum of 64 gray shades, it is hard to exam the images, particularly for weak spots.  MicroVigene allows you  to view the image spots in 3D surfaces, which shows clearly whether the spots are located correctly.  Our data accuracy has been significantly improved since we deployed the 3D tools.

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A batch process can be done by selecting a set of files from different folders.  By default, one template applies to all the files. You can specify different templates for some individual or group of files.  You can also select the operation from predefined set or create your own operations through plug-in. (see next FAQ).

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MicroVigene allows customers to write simple DLLs in C# or VB.Net that can plug into MicroVigene.  For example, you can create a plug-in to retrieve all spot measurements from MicroVigene and directly output them to your own database or perform further statistical analysis.  The plug-in interface and sample are available to the registered customers.

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MicroVigene supports any image layout up to three levels of hierarchies.  In other words, an image can contain any number row and column of blocks; each block can contains rows and columns of main grid; and each main grid in turn can contain rows and columns of sub grid.

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Yes, MicroVigene allows you to have configurable objects.  Each object, which contains a block, can have its own number of rows and columns of main grid or sub-grid and own settings to locate grid and spots.

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MicroVigene currently output data in text, Excel, and XML.  You can easily create a plug-in to output any format as you wish (see three FAQ above).

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Grid and spots can be saved in .vgs extension with the same name as image file. You can open the saved grid and spots via menu Open/Image or Open/Spots

Note the difference between Open/Image and Open/Spots.  When open via Open/Image, it first loads the corresponding image, then overlays grid and spots on top; while open via Open/Spot, it will first delete any exist grid and spots and then load grid and spots  and overlay them on top.

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MicroVigene is probably the only Microarray image software has a built-in 3D interactive viewing tool.  It allows you to view how accurately the spots are located.  The accuracy of the spot location has been drastically increased since we have had this tool.

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Yes, the data points in the correlation plot are linked to spots in the image.  If you click the point, the corresponding spot pair is highlighted and vice versa.

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Yes, each row in the fold change is linked to a spot-pair in the image.  If you click a row, the corresponding spot pair is highlighted and vice versa.

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MicroVigene can read tab-delimited plate-map text files to associate GeneID with each spot.  The plate-map sample files will be included.

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When a spot signal is less than one standard derivation of the background, the signal is insignificant.  MicroVigene gives you the option to set the minimal signal in unit of standard derivation.  For example, if the value is set to 0.1, any signal below 0.1 of its standard derivation, will be reset to 0.1*(standard derivation). If it is set to a negative number, no minimal will be set.

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MicroVigene can detect and remove dust automatically.  Correctly detecting dusts is an important and challenging task in Microarray image analysis.  MicroVigene allows you to set the three dust parameters (threshold, maximum diameter, and minimum mean) to detect both weak and strong dusts.

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Yes, you can select the tool bar to flag the bad spots by clicking them or use rubber bands them.

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Yes, though we certainly hope that you never need to do so, MicroVigene does allow you to select a spot by clicking it and then moving the spot with arrow keys. Don't forget to recalculate signal under Analysis menu after finishing moving all spots.

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Manual move is strongly discouraged. In most cases, it can be avoided by twisting the settings in Spot page of the Option dialog.  Nevertheless, MicroVigene does allow you to select a spot by clicking it then move the spot with arrow keys.  Please remember to recalculate signal under Analysis menu after finishing moving all spots.

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Yes, based on the name convention specified, MicroVigene can overlay the pair automatically upon load and close reference-sample pair.  You only need to find grid-spots from the composite image.  The correlation and fold change can be viewed directly from the composite image.

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If the image is very noise, MicroVigene cannot find enough good spots or pick up too many fake spots to align the grid properly. Click menu Analysis/Find/Boundary Spots to find spots and boundary. If you see too many fake spots were identified, decrease the sensitivity and/or increase the sort criteria then try again. On another hand, if not enough spots were found near boundary, increase the sensitivity and try again. If it still fails, right click in the ROI and select Show anchor from the popup menu. Drag the anchors such that they are aligned with the boundary, then click button Go on the toolbar to find grid and spots.  If the image has a clear grid pattern and for any reason it does not align the grid correctly, please email us the image or let us know, we will look into and solve the problem.  Please don't just use the anchor to fix the problem, because we would like to know why not. Remember, don't be hard on yourself, we are here to make your life easy.

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We believe MicroVigene delivers the best quality, performance, flexibility, and extensibility.  We knew there are over a dozen of microarray image software on the market before we started to develop MicroVigene.  It would make no sense to have another "me-too" software package if it could not be the best. Please send us your sample images, good or bad, we will send you the analysis data from MicroVigene. The image analysis result will speak for itself.  We are confident that when you see the difference between MicroVigene and other software packages there is no need to persuade any of our customers switching to MicroVigene.  All we want to say is: welcome!

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