Regulación general aplicada al medicamento

ImageTracker has two main image manipulation modes: filtering and processing. Fil- tering applies an operation on images as they are displayed in the ImageTracker image panel, and results are visible instantly. (This is similar to filtering in other imaging applications such as ImageJ or Gimp.) Processing typically involves more complex com- putations that create a new set of output images. The output images must be loaded into ImageTracker to see the results of a processing task, though this is often handled automatically by ImageTracker.

Filtering is often used to prepare an image set for processing. The list at the top of the Images tab in the control panel contains the names of all filters that are being actively applied. The Image Files filter is a special filter that is always present and can be used to load image files as shown above. Other filters can be added to the list by selecting them from the Filters menu. Filters are chained and applied in the order that they appear in this list. Selecting any filter in the filter list displays that filter’s configuration in the panel below. Changes to filter parameters are visible instantly in the image window.

Figure A.4: Result of applying the threshold filter to a fluorescence microscopy image of a mitotic spindle. The threshold filter limits the range of intensities present in an image. Microscopy image from Lisa Cameron.

filter from the filter list. The Image Files filter is a special filter that cannot be removed (with no image files loaded there is no image data to filter). The Clear button resets the filter list to its initial state with no filters or image files loaded.

A.4.1

Threshold

The threshold filter sets any pixels from an input image that lie outside an intensity range to zero (black). An example of applying a threshold is shown in Figure A.4. The threshold control panel has the following controls.

Upper and Lower Bound Sliders that adjust the range of pixel intensities that pass through the threshold filter.

Range Controls the range of pixel intensities displayed on the threshold bound sliders. There are presets for 8-bit and 16-bit images, and an option for setting the slider range to match the intensities of the current input image.

(a) (b)

Figure A.5: a) Result of applying the Gaussian filter to a fluorescence microscopy image of a mitotic spindle. A first order Gaussian is applied along the x-axis, while a zeroth order Gaussian is used on the y-axis. b) Result of applying the gradient magnitude filter to the same image.

A.4.2

Gaussian

The Gaussian filter convolves an input image with a Gaussian kernel. Convolution with a zero-order Gaussian smooths (blurs) the image. The scale (standard deviation) of the Gaussian filter determines the degree of smoothing applied. Convolution with a first-order Gaussian along one dimension computes the derivative of the image along that dimension at the scale of the Gaussian. An example of applying a Gaussian filter is shown in Figure A.5a. The Gaussian filter control panel has the following controls.

X- and Y-direction Scale Sliders that select the Gaussian kernel scale along the x and y dimension of the input image. The scale determines the standard deviation of the Gaussian kernel in pixel units.

Lock When the Lock button is depressed, the X- and Y-direction Scale sliders will move together. Otherwise, the scales can be adjusted independently.

X- and Y-direction Order Controls the order of the Gaussian filter applied along each dimension. Zeroth, first, and second order Gaussians can be selected.

A.4.3

Gradient Magnitude

The Gradient Magnitude filter is often used to find edges in an image. The gradient (first derivative) of the input image is computed in each direction with a Gaussian kernel at a spatial scale (see Section A.4.2), yieldingIx andIy. The gradient magnitude is then

given by: G = pI2

x +Iy2. Edges, regions with large gradients, are emphasized by this

operation. An example of applying a Gradient Magnitude filter is shown in Figure A.5b. The Gradient Magnitude control panel has the following controls.

Scale The spatial scale of the Gaussian kernels used in gradient computation. Larger values find the edges of larger image features.

Normalize Across Scale When this option is checked, the brightness of the filtered image will not fade at larger spatial scales. When this option is disabled, use the Window/Contrast control to rescale the contrast if the image becomes dim.

A.4.4

Logarithm

The Logarithm filter takes the logarithm (base 10) of an image. Zero values in the input image are mapped to zero values in the output image. This filter has no options.

A.4.5

Flat-field

As described in detail in Section 2.3, constant image flat-fielding and subtraction are techniques commonly used in microscopy to correct for imaging artifacts. Flat-fielding divides input images by a constant image to correct for uneven illumination or occluding objects in bright-field imaging. An appropriate flat-field image would be an image of a blank slide or ”bright” calibration (or the mean of several such images) or the trans- mission map obtained from the Remove Occlusions process (discussed in Section A.5.1). Figure A.6 shows an example of applying a flat-field filter to an image.

Figure A.6: Result of applying a flat-field filter to a bright-field image of cilia beating on a cell culture. The flat-fielding has removed the non-moving cell bodies from the image.

Background subtraction subtracts a constant image to correct for sensor noise or background signal. An appropriate background image would be a ”dark” calibration image taken with the lamp off (or the mean of several such images). The Flat-field control panel enables using either or both of these techniques simultaneously. When both background, B, and flat-field, F, images are supplied, the output image, O, is given by: O = I−B

F . That is, the background image is subtracted from the input

image before flat-fielding is applied.

The following controls compose the Flat-field control panel.

Flat Image Specifies whether flat-fielding should be applied. The control prompts for the flat-field image when checked for the first time. To select a different flat-field image, use the Browse button.

Background Image Specifies whether background subtraction should be applied. The control prompts for the background image when checked for the first time. To

select a different background image, use the Browse button.

A.4.6

Saving Filter Images

A set of filtered images can be saved by selecting File → Save Filter Images from the menu. This will save the output from the filter pipeline that is displayed in the image filter list, not the visualization displayed in the image panel. The Save Filter Images dialog includes controls for specifying the output directory and file naming convention to use. There are also several output options:

Pixel Type Specifies the data type of pixels in the output images. Use 16-bit for images with intensities in the normal camera output range (floating point values will be truncated). Use floating point for computed images that have small fractional values.

Rescale Intensities When this box is checked, the output image intensities will be rescaled to match the full range allowed by the output pixel type.

ImageTracker can save image files in any format supported by ITK. This includes TIFF, PNG, JPG, MHA, and VTK among many others. Some file types (e.g. TIFF and PNG) only allow integer pixel type data, and saving floating point pixel data will likely produce an error. When saving floating point images, select a file extension that has floating point support (e.g. MHA and VTK).