Frida Software User Manual

General Instructions

  1. Go to this webpage: (
  2. If you need sample images, click on the Download link in this page, or get them from TMAJ. 
  3. Click the Launch Program Link.
    Note: We assume that you have already downloaded the Java 6 Runtime Environment (JRE) before you start this step. If not, click the given in this instruction to install it. You only have to install Java once.
  4. Create or open an existing project:
  5. See the Masks section below and create as many masks as necessary.  A Mask is a defined area of interest for a region.  It might be a color, or a circled-area, or anything that makes some pixels in the image included, and other pixels excluded.
    1. Look in the New Masks area, and then click the New Button to add a new mask. 
    2. Give the Mask a descriptive name. For example, if you had a Color Mask and you were going to select-only brown, you might want to call the Mask "brown".  You can always change the mask name later using the Edit button.
    3. Choose a Mask type: Color, Lasso, or Meta Mask.  A Color Masks let you select a color range in each image to analyze.  A Lasso Mask lets you include/exclude regions of the image you want to analyze.  A Meta Mask is a logic statement that lets you combine information from the Color and Lasso Masks.  More information on each is provided below.
    4. To generate the full collection of analysis values, check the Use Full Analysis checkbox. . A full analysis generates multiple numbers for each mask including Mask area, minimum intensity (IntMin), maximum intensity (IntMax), sum of intensity (IntSum), mean intensity (IntMean) and median intensity (IntMedian) .   If you have not choosen "Set Full Analysis", A smaller analysis that generates only an Area value for each Mask is performed.  You can tell which masks use the "full analysis" because they will appear in bold. 
    5. To configure the Mask, double-click the Mask name or click the Open Button.
  6. Before clicking the Run Analysis Button, always save the Project.  It is a good idea to save the Project file frequently and perhaps with different names.  The Project file saves all of the created masks including all of the lasso parameters. Save your analysis by going to the menu, then Project, then clicking save.  You can then go back to this analysis at any time.
  7. Click the Run Analysis Button. You will be prompted for a file in which the program will write the results.  By default, the export format is Spreadsheet.  The Spreadsheet option means the file will be written to a tab-delimited text file that can be opened in Excel for futher analysis.  An XML format is also available.  The XML format is used to export the results into TMAJ.


Color Masks

Color masks are also known as pixel threshold masks.  To add a new Color Mask, Right Click in the Masks box and select New.  In the Add Mask bar, name this some sort of descriptive term such as “Brown” or “Blue” and select Color Mask. 

In the color mask, you will simply set an HSB (HSV- Hue, Saturation, Brightness) color range for the mask. To begin identifying the color of interest, click the Open… button to open 1 or more images. Use the Hand Button to select a pixel in the image that you want for that Mask. Every time you select a pixel using the "hand" tool, the range will be expanded to include this pixel and all pixels between it and the previously selected range. All pixels in the range will be highlighted in RED.  A threshold can also be expanded by moving the Min/Max Hue, Sat and Bri slides to include additional space. You cannot change the values by typing new values into the number boxes.

Lasso Masks

Lasso masks are also known as freehand masks.  To add a new Lasso Mask, Right Click in the Masks box and select New.  In the Add Mask bar, name this some sort of descriptive term such as “Glands” or “Removed,” and select Lasso Mask. 

Click a navigation button (one of the arrows) to begin cycling through all of your images.  Drawa lasso around any region of interest.  If you have two or more regions of interest, hold down the shift key.  If you do not hold down the shift key, each new lasso will replace the old lasso. Click the Close Button when you are finished.  The Default if no Lasso Choice controls what is recorded in this mask if the user fails to draw a lasso for a certain image. Setting it to nothing excludes everything on the image if the user doesn't circle a lasso.  Since this step usually takes the longest in the program, you may want to save the project periodically.

Image Tools

Zoom Button: The Zoom button lets you zoom in (left mouse click) or zoom out (right mouse click) on an area of interest. It is a good idea to zoom in on the images to the point that the image appears pixilated to identify individual pixels to select.

Mask Box : This toggles the mask you have created.  Uncheck this box if you wish to see the original image (If this is unchecked, the pixels in the mask won't be highlighted.)  Toggling on/off can be performed for each Mask that has been generated.  The Color of the Mask and the Order relative to other Masks can also be changed by left clicking on the value.

Meta Masks

A Meta Mask is a logic statement that allows for the combination of information in already defined masks.  Meta masks are also called "masks of masks".  To generate a Meta Mask, right click in the Masks box, select New and name the Mask based on what function it will serve and select Meta Mask.  Then right click on the Meta Mask and click Configure.  Press the Add line to generate statements.

Example: Let's say you created a Color Mask called BROWN, and you created a Lasso Mask which you called CIRCLED_CANCER_AREA. You only wanted to see the area that was both BROWN AND in the CIRCLED_CANCER_AREA. And means Logical And.  If you choose "And", the Meta-Mask will identify only regions that are in BOTH of the selected Masks .  If you use Logical Or, the meta-mask will include regions that are in both thetwo selected Masks.  For this example, You would add a Meta Mask that has:
[ -----] [WHAT IS IN] BROWN

If you had accidently selected OR, your meta-mask would include areas that are both in the brown area and in the circled cancer area, as opposed to the area where they both intersect (and). 

Meta Masks can include a number of previously made Color, Lasso or other Meta Masks.  The logic options are AND/OR and what is in/what is NOT in.
Close the Meta Mask window after you are complete. You are then ready to use this mask.

How to move Masks to Different Projects

The Project file is a xml file and can be opened in a Textpad or WordPad program.  Each Mask is shown with a series of <> symbols.  A Mask can be moved from one Project to another by simply copying the Mask from the donor Proect and pasting the Mask into the acceptor Project.
The example below is the entire Mask for a color named "Blue".  It is portable from one Project to another.