Frida Software User Manual
General Instructions
- Go to this webpage: (http://bui3.win.ad.jhu.edu/frida/)
- If you need sample images, click on the Download link in this
page, or get them from TMAJ.
- 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.
- Create or open an existing project:
- To create a new project: If
you need to create a new project, you have 2 options. You may
either create a project in the database, or you may create on on your
local machine. The advantage of keeping a project in the database
is that all your data will be in one central place.
- To create a project in the database, go to the menu, then
click New,
then click New Project in Database. To create a file on your
local
hard drive, click "Create Project in File". If you choose the
"Create
Project in File" option, all the data for your project will be in one
file; the database will not be used.
- Go to the folder that contains all the images
that you
plan to analyze. The project file will be in the same directory that
contains the images your wish to analyze.
- Choose a name for your project, and then click
the
okay button.
- To use an existing project: If you have an existing project
(generated color masks,
lasso masks, etc), go to the menu, then projects, then click
Open. Locate your project file in the directory and then open it.
- 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.
- Look in the New Masks area, and then click
the New Button to add a new mask.
- 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.
- 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.
- 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.
- To configure the Mask, double-click the Mask name or click the
Open Button.
- 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.
- 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.
Masks
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
[AND] [WHAT IS IN] CIRCLED_CANCER_AREA
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.
<COLOR-MASK>
<NAME>Blue</NAME>
<IS-ANALYZED>yes</IS-ANALYZED>
<HUE>
<START>160</START>
<END>215</END>
</HUE>
<SAT>
<START>64</START>
<END>216</END>
</SAT>
<BRI>
<START>88</START>
<END>255</END>
</BRI>
</COLOR-MASK>