Copy Draw Circle Roi Over Slices Matlab

Part 2: Manage Regions of Interest (ROI) and Annotate Images³

Now that you are an practiced on the selecting tools, you may be wondering what you can do with this new-found knowledge. On days 4 and 5 you will be simulating the workflow of a professional person research project involving changes in Arctic Sea Ice over time. The goal of the investigation is to measure and graph changes in the monthly average Arctic Body of water Ice extent over a period of several years, and for several specific written report regions. Yous may already be familiar with the data used in the investigation, only the workflow will be quite different from what you may accept done in the past. It will hinge on a very powerful organizational tool built into ImageJ chosen the ROI Manager. As you think, ROI stands for "Region Of Interest"—simply a fancy proper name for a selection.

Earlier working with the ROI Manager, information technology'south helpful to be aware of some of the other things you tin can exercise to manipulate selections (ROIs).

The Selection Submenu

A number of useful pick-related functions are found nether the Edit > Selection submenu.

Use the Pasadena image to make a selection, and then see what each of these ROI Manipulations does:

• Fit Spline – Fits a cubic spline curve to a polygon or polyline (segmented line) selection.
• Fit Circle – Fits a circumvolve to a multipoint, segmented line, angle, or area option. With closed shapes, the circumvolve has the same surface area and centroid (center) every bit the original selection.
• Fit Ellipse – Replaces an area selection with the best fit ellipse. The ellipse will have the same surface area, orientation, and centroid every bit the original selection.
• Convex Hull – Replaces a polygon or freehand selection with its convex hull. Think of drawing the polygon on a board, pounding in nails at each vertex, and putting a rubber band around the nails. The polygon shape fabricated by the rubber ring is a convex hull.
• Brand Inverse – Creates an inverse selection. The pixels that were outside the pick are all at present inside the option. This is very useful when y'all desire to make measurements of the pixels in complementary regions of the image. (Light-green versus non green, for instance. Select the green pixels, then choose Make Inverse to select the non-greenish pixels.)
• Create Choice – Creates a selection from a thresholded image.
• Create Mask – Creates a new viii-chip image called "Mask" whose pixels have a value of 255 within the selection and 0 outside the selection.
• Backdrop – Opens a dialog box that lets yous set the stroke (line) color, fill colour, and width of the option outline. The bachelor selection colors are black, white, cyan, magenta, yellowish, red, green, blueish, and orangish.
• Rotate – Rotates a choice the specified number of degrees.
• Overstate – Grows (expands) a choice by a specified number of pixels. Positive values make the option larger and negative values get in smaller.
• Make Ring – Takes an area selection and makes a band around the perimeter a specified number of pixels wide. For case, if you select a circle and so choose Make Ring, the selection will resemble a donut (D'oh!)
• Specify – Opens a dialog box that lets y'all specify the pinnacle, width, and location of a rectangular or oval selection.
• Straighten – Straightens curved selections made with the segmented line option tool.
  • Open up the NileBend sample prototype.
  • Use the segmented line tool to trace the route of the river.
  • Choose Selection > Straighten (and be amazed).
• To Bounding Box – Converts a non-rectangular selection to the smallest rectangle choice that would completely incorporate the original option.
• Line to Area – Converts a line selection more than one pixel wide to a traced outline.
• Surface area to Line – Converts an surface area selection to a line selection by removing the concluding segment completed while making the selection.

The ROI Manager

The ROI (Region Of Interest) Manager is a handy utility that not only helps you to save and keep rails of different selected regions, but it includes powerful set operations (spousal relationship, intersection, etc.) that can accomplish difficult and ho-hum tasks in a couple of clicks. There won't be time to thoroughly explore all its capabilities, but you should get a hint of what the ROI Manager can do.

• Even so working with the Pasadena aerial image, zoom in on the building shown hither.

  

  
  If you wanted to select the outline of this building, you could exercise information technology as a compound selection by calculation together selections made with the rectangle and circle tools, which would require pressing and releasing modifier keys at just the right time or you mess it upwardly and have to start over again. Sounds like fun, right? This is a perfect task to attain using the ROI Managing director.
  
• Employ the rectangular option tool to select the large rectangular section on the left.
  
• Choose Edit > Option > Add together to Manager or use its keyboard shortcut. This opens the ROI Manager window, which lists the selection you only made with a series number.
  
• Click anywhere outside the selection rectangle on the image to abolish the rectangular selection.
• In the ROI Manager window, click the serial number of the selection in the left-hand column. Voila— the pick isn't gone, it'south just being managed!
• The series number isn't very useful for identifying the choice, and then click the Rename push button in the ROI Manager window and requite the selection a catchy proper name like "Rectangle 1".
• Using the rectangle tool, select the other big rectangular section on tiptop. Make certain the bottom edge extends all the way downwardly to the point where the curved outer wall begins.
  
• Add together the 2d choice to the ROI Manager and proper noun it Rectangle 2.
• Brand a third rectangular selection to bring together these two parts of the building together. Make sure this selection overlaps the areas covered past the other ii past a piddling. Add this pick to the ROI Director and rename information technology.
• Make a circular selection of the round part of the edifice, selecting from the center of the smaller circle on the roof. (Employ modifier keys to select the circumvolve from the center!) Add together the pick to the ROI Manager and rename it.
• In the ROI Director, click your way down the list on the left and spotter each of your iv ROIs lite upwardly.
• What we want is to select the whole building at once. Drag downwards the listing or shift-click to select all 4 named ROIs. Only one will appear active on the paradigm. If you lot cheque the Evidence All option at the lesser of the ROI Director window all four ROIs will appear.
• To merge the four selections into 1, click the More button at the bottom of the ROI Managing director and choose the Or (Combine) selection from the pop-up menu.
• Uncheck the Prove All selection. You should now meet a unmarried outline effectually the building.
• Click the Add push button to add this new selection to the ROI Manager, and rename it. If you don't need the four smaller selections, you lot can delete them from the ROI Director. Just highlight and click Delete.
• At present you can do anything with this option that you want—use it to draw the building's outline, measure the roof area, relieve the ROI file (Open and Salvage are both on the More popup menu), transfer the ROI to a different prototype, and much more than.
• If you want to try downloading and opening a ROI file in ImageJ, here's the one created for this exercise. Building Footprint ROI (Cipher Annal 397bytes Jul20 xi)

Image Note

Annotation is the process of calculation (drawing) points, lines, arrows, shapes, and text on images to identify important features or provide boosted information about the epitome. There are 2 basic types of note—destructive and non-subversive.

Destructive Note

Destructive annotation is named for the fact that you are cartoon directly on the image. In other words, you are replacing the original pixel data with new pixel values that represent the colors of the graphic elements you are adding. This is fine for any work where you exercise non need to get at the original epitome data. Tip: Always work on a copy of your image and keep an original or untouched copy in a prophylactic place. Destructive note can't be undone.

For every betoken, line, pointer, or shape you want to add:

• Make a selection
• To set up the drawing color, double-click the color picker tool on the ImageJ toolbar and choose a foreground color.
• To set up the width of line selections, cull Edit > Options > Line Width.
• Choose Edit > Draw to draw the point(s), line, or shape outline in the color and width you specified.
• Choose Edit > Fill to fill expanse selections with the foreground colour.
• Choose Edit > Articulate to fill within the pick with the background color, which is usually white.

To add text annotations.

• Double-click the Text tool to open the font options dialog box:

  

  
  
• Gear up the Font, Size, Way, and smoothing choice.
• Text is drawn in the foreground color. Set the text color if necessary. (Tip: The foreground color is the color that appears in the eyedropper icon for the color picker button on the toolbar.)
• Click on the image where yous desire to place the text (it doesn't accept to be verbal, you can move the text choice anywhere at any time as long as the selection remains active. You can even change the font settings and color.)
• When you take the text element the fashion you want it, choose Edit > Draw. The text is drawn on the image in the foreground color.
• Don't forget elements similar scale bars and scale confined—you should accept learned how to add together those in an before exercise.

Non-Subversive Annotation

In non-destructive note, the graphic elements (Including other images) are added to a transparent overlay layer, and this layer can be turned on or off. The procedure is virtually identical to subversive notation, except:

• Make the selection, and so cull Image > Overlay > Add together Selection. If your selection was a signal, line, or shape, you will come across this dialog box. Make the appropriate settings and click OK to add the selection to the overlay.

  

  
  
• If the selection is text, yous volition see this dialog box. Make the appropriate settings and click OK to add together the selection to the overlay.

  

  
  
• Caution: At that place is only one overlay—if you cheque the New overlay option, everything on the electric current overlay will be lost.
• The simply prototype format that supports the overlays is TIFF. If you are working with an annotated image and don't want it "flattened" (converted from non-destructive to destructive past moving the graphic elements from the overlay and cartoon them on the image.
• Y'all can't really edit your overlay. If you make a mistake, y'all pretty much need to delete it and start over. However, if yous build up the elements of your overlays using the ROI Director, you can get the elements "only right" before you add them to the overlay. Note the 2 items on the Image > Overlay submenu: From ROI Managing director and To ROI Manager.
• Always utilise Hide Overlay and to turn the overlay brandish on and off.
• Remove Overlay deletes the overlay layer.
• Flatten merges the overlay with the image. This is useful when you need to save the image in a format that does not support overlays (basically, everything except TIFF.)

Your Consignment: Define Written report Areas and Save Them As Regions of Interest (ROI)

1. Go to NEO (NASA Globe Observations) and download two images of interest to you. Make sure they are the same size. Choose two different datasets that make sense to compare.
2. Spatially calibrate each prototype.
3. Choose one of the images to ascertain and select three written report areas. Save and label each choice as to the Region of Interest (ROI) Manager.
4. Open and use the ROI to the 2nd image and mensurate the areas.
5. Use an overlay to annotate your epitome.
6. Accept a screen shot showing your images with selections along with the Results window and post it to the Role 2: Share and Discuss Page. Then describe equally much as you tin can near what you analyzed.
7. Appoint in an online discussion, sharing your ideas almost using Regions of Involvement (ROI) in classroom investigations.

Source

^oneAdapted from Earth Exploration Toolbook chapter instructions under Creative Commons license Attribution-NonCommercial-ShareAlike 1.0.
²Adapted from Optics in the Sky Ii online course materials, Copyright 2010, TERC. All rights reserved.
³New material developed for Earth Assay Techniques, Copyright 2011, TERC. All rights reserved.

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Source: https://serc.carleton.edu/earth_analysis/image_analysis/advanced/day_3_part_2.html

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