Opening and loading image files

From MIPAV
Jump to: navigation, search

Opening image files

MIPAV displays images in windows, or frames, that you can move or arrange around the desktop. You can display as many image datasets as needed as long as your computer has enough allocated memory.
Note: The amount of memory required depends on the number of image datasets that are open and the size of each image file. For more information, refer to "Managing memory resources".

You can either open or load an image file. When you open an image file, MIPAV displays the image in a new image window. Loading an image file imports the file into an image window in which another image file is open. In other words, two image files share a common image window.

Sample images to starts with MIPAV can be found here - Sample images.

Understanding image windows

An image window consists of a title bar and an image itself.

The MIPAV ImageJ toolbar

The title bar displays:

  • the image file name, e.g. "DTI_TEST";
  • the number of the current slice and the total number of slices in the dataset, e.g. 32/69z and 1/16t;
  • the magnification level, e.g. M:3.0.
  • The number of the current slice is also shown in the lower left corner of the image.

You can move an image window around your desktop by clicking the title bar and dragging the window to a new location.

Sometimes, depending on the view, a toolbar or menu bar also appears in the image window. For example, the image window using thelight box view contains a toolbar and menu bar. See also Displaying images using the lightbox view.

Image A and Image B

In MIPAV, the first image opened in an image window is referred to as Image A. When you load, or import, a second image in the same window, MIPAV refers to the second image as Image B.

Note: The abbreviations (A) or (B) appear after some commands. (A), which is the abbreviation for "Image A," indicates that the option is applied to the first image opened in an image window. (B), which is the abbreviation for "Image B," indicates that the option is applied to second image loaded in the image window. For example, if you select Close Image (B), MIPAV closes the second image (Image B) that was loaded in the image window.

Supported formats

You can use MIPAV to open or load files of a variety of medical and generic graphics and multimedia file formats. Table 1 lists the format, extension, and whether MIPAV can read or write files of a particular format. The extension, which is the last few characters of a file name including the period, indicates the file format. For example, in the file name DOE255.ima, the extension .ima indicates that the file is stored in DICOM format. In the table, the Read column indicates that MIPAV can display image files of a particular format. When a file is read, it is stored in main memory so that MIPAV can access it. The Write column means that MIPAV can copy the data from the memory to a storage destination, such as your hard disk. In this context, "write" is synonymous to "save".

For more information on file formats, the list of supported formats and other information, refer to File formats supported by MIPAV and Image formats descriptions.

Image Browser

Choose Image Filter dialog box

You can select the image formats to display using the File > Open Image(A) > Image Browser menu. This opens the Choose Image Filter dialog box. In this dialog box, use the check boxes to select the image types which you would like to use in MIPAV.


Image Browser

Select All

Selects all image types.

Clear

Removes selection.
Applies the image type selection to MIPAV.

Cancel

Disregards any changes you made in this dialog box and closes the dialog box.

Opening image files

The Open Image A from disk menu allows you to open an image which is stored on your hard drive (or a network drive).

Open Image A


Open Image A menu

provides you with additional options such as to open a single image file, or image sequence, or Leica series images - the images that were taken on a Leica microscope. You can also call Create Blank Image to create a blank image (refer to "Creating new images").
To open an image file or multifiles

Open as multifile option

The Open Image dialog box, which appears after you select File > Open Image(A), has an option that allows you to open the image as a multifile.

Open Image(A), is as multifile


Multifiles are image datasets that are composed of multiple files. To open an image as a multifile:

  1. Select File > Open Image(A) from disk. The Open Image dialog box opens.
  2. Navigate to the directory where the file is stored.
  3. Select an image file.
  4. To open the image file as a multifile, select the Open as multifile box. The name of the image appears in File Name.

If you can't find the image,check the files types listed in Files of Type near the bottom of the dialog box. If the file type you are looking for does not appear in Files of Type, select All Files or All.

To form a 4D dataset in Analyze format, use Open as multifile to open a series of individual 3D Analyze, formatted, consecutively ordered images. For example, you can use Open as multifile to open an array of TIFF, JPEG, BMP, etc., files if their file names meet the following format: foo_001.tiff, foo_002.tiff, foo_003, etc. where foo is the name of the file.

MIPAV window

Expanded MIPAV window

After the first image is opened, the MIPAV window changes. It includes more menus, the title bar displays more information, and tool bars appear. Because the MIPAV window is context sensitive, it displays or hides commands on the menus depending on the characteristics of the image file that is opened. If you opened a dataset file that contains more than one image, an image slice slider also appears.

If you prefer for MIPAV to use the style of Open and Save dialog boxes that are used by the operating system (e.g., Microsoft Windows, Unix, or Apple) on your computer, read the section on "Using platform-specific Open and Save dialog boxes" (TBD).

Loading image files

When you choose the Load an image file command, MIPAV imports a new file into an existing image window (Image A). The loaded image (Image B) shares the same window with the image file that was originally there. Loading a file allows you to compare two image datasets.

To load an Image B file:

  1. Open the first image by selecting File > Open Image(A) from disk. The image appears in an image window.
  2. Select the title bar of the image window (in this case, the image that you just opened) in which you want to load another image.
  3. Select one of the following:
    • File > Load Image (B) > From Frame to load another image dataset from an already opened image dataset;
    • File > Load Image (B) > From File to load another image dataset;
    • File > Load Image (B) > Create a Blank Image to create a blank image.
  4. If you chose Image (B) from File, the Open dialog box appears. Select the image file you want to load, and click OK.


If MIPAV does not recognize the type of file based on its extension, the Choose Image Filter dialog box opens (see also Image Browser). Then, select the file type and click OK.

Opening Image A and Image B. Alphablending slider


Alphablending

As the image file is loading, a pop-up window appears with the status. When the image file finishes loading, it appears in the image window. At this point, take note of several changes:

  • MIPAV pseudo-color was applied to the images in the image frame. The pseudo-color indicates that two images are loaded in the same image frame.
  • In the MIPAV window, the Active Image and Alphablending slider appears. The slider allows you to control which image is displayed in the foreground of the window. The image in the foreground is the active image. You can adjust the translucency of the alpha channels in each image using the technique.
  • If you chose Image (B) from Frame, the Load Image onto <file name> opens. Select one of the images in Set as Image (B), and then click OK. The image is loaded onto the first image file.

Note: MIPAV recognizes files types by the file extension. For example, if you select an image named "Smith.tiff", MIPAV tries to open the file as a TIFF file. If that image is actually a JPEG file and mistakenly has the TIFF extension, MIPAV fails to open the file.

Active image

In the MIPAV window, the Active Image and Alphablending slider allows you to control which image is displayed in the foreground of the window. The image in the foreground is called the active image. To select the active image, click the radio-button corresponding to the image (Image A or Image B). In order to compare images, can adjust the alpha channels in each image using the slider.

See also: