Electron Tomography Toolbox for Amira

An Amira module can have an arbitrary amount of input parameters. These input parameters are called ports and shown in the properties area of the Amira window when a module is selected. To simplify the definition of the parameter values, ports can be buttons, radio boxes, sliders, fields, drop down menus, checkboxes, file choosers, colormaps or tab bars.

A button is a GUI element which allows you to start a computation or another event.

A radio box provides 2 or more options for a parameter where you can choose only one of them.

A slider is a GUI element for a numerical parameter which has to be in a particular range.

A number field is a GUI element which allows you to enter an arbitrary number.

A drop down menu (also called popup menu) contains an arbitrary number of entries where you can choose one of them.

A checkbox is used for parameters which have only 2 states like ?on/ off? or ?visible/not visible?.

A file chooser is used to define a directory and a file. This file is used as an input or output file.

A colormap is used to define a specific color either by choosing it from a color palette or by defining the particular values for RGB or HSV.

A tab bar provides the possibility to separate ports according to their usage.

Loads ccp4 density map files with default file extension .map in little endian byte ordering.

Loads em files with default file extension .em in little endian and big endian byte ordering.

Loads imagic files with default file extension .img in little endian and big endian byte ordering.

Loads mrc stacks with default file extension .mrc in little endian byte ordering.

Loads spider files with default file extension .spi in big endian byte ordering.

Writes ccp4 density map files with default file extension .map.

Writes em files with default file extension .em.

Writes imagic files with default file extension .img.

Writes mrc files with default file extension .mrc.

Writes spider files with default file extension .spi.

Projects N slices in the 'z' direction to improve the SNR.

Converts a motive-list file into a STAR file and the other way round.

Converts float or integer input data to binary data.

Converts float, binary or integer input data within a given range to integer data.

Converts float, binary or integer input data to float data.

Adjusts the intensity values of the image between 0 and 1.

Inverts the contrast of the image.

Sets the intensity values outside a user-defined range either to 0 or the range values.

Computes a 2D projection from a 3D image under given angles or the given camera position.

Reduces the number of pixels by a factor of 2 in all dimensions.

Rotates the input data by the given Euler angles, according to the TOM-package conventions.

Is used to calculate the rotation difference between two objects.

Applies the bilateral filter to the input data.
(Jiang,W., Baker,M. L.,Wu,Q., Bajaj,C. and Chiu,W. (2003). Applications of a bilateral denoising filter in biological electron microscopy.
J Struct Biol. 144:114-122)

Filters the input data in the Fourier space with four given values; the amount of cut-off in the high and the low frequency range, as well as the desired Gaussian fall-off to reduce ringing artifacts.

The module is only available in the Linux version.

Convolutes the input data with the user defined filter function (kernel).

Edge and Skeletonization filter. Useful for visualizing flow-like structures.

The module is only available in the Linux version.

Is used to pick positions on a surface or slice. These positions can be stored in a so called motive-list file, according to the TOM-Package convention.

Extracts labels with defined object properties.

First it applies a threshold on the input data, to generate a binary image. Second it labels all the coherent islands with distinct "labels".

Is used to pick labels with the mouse and generates a binary mask.

Applies the watershed segmentation to the input data.

Creates a binary mask from labeled input data.

Is used to widen the binary mask with a sphere kernel or a user defined kernel.

Is used to thin the binary mask with a sphere or a user defined kernel.

Is used to visualize molecules at positions defined in the motive-list. Additionally molecules can be selected or removed and a new motive-list can be generated.

Is used to visualize high resolved molecules at given positions in a tomogram without upsampling the tomogram or downsampling the molecules.

Is used to generate photorealistic images with shadows and reflections (raytracing).

Applies the bilateral filter to the input data.
(Jiang,W., Baker,M. L.,Wu,Q., Bajaj,C. and Chiu,W. (2003). Applications of a bilateral denoising filter in biological electron microscopy.
J Struct Biol. 144:114-122)

Loads ccp4 density madiv files with default file extension .map in little endian byte ordering.

Writes ccp4 density map files with default file extension .map.

Is used to pick positions on a surface or slice. These positions can be stored in a so called motive-list file, according to the TOM-Package convention.

Projects N slices in the 'z' direction to improve the SNR.

Converts a motive-list file into a STAR file and the other way round.

Converts float or integer input data to binary data.

Converts float, binary or integer input data within a given range to integer data.

Converts float, binary or integer input data to float data.

Creates a binary mask from labeled input data.

Is used to widen the binary mask with a sphere kernel or a user defined kernel.

Loads em files with default file extension .em in little endian and big endian byte ordering.

Writes em files with default file extension .em.

Is used to thin the binary mask with a sphere or a user defined kernel.

Extracts labels with defined object properties.

Filters the input data in the Fourier space with four given values; the amount of cut-off in the high and the low frequency range, as well as the desired Gaussian fall-off to reduce ringing artifacts.

The module is only available in the Linux version.

Adjusts the intensity values of the image between 0 and 1.

Loads imagic files with default file extension .img in little endian and big endian byte ordering.

Writes imagic files with default file extension .img.

Inverts the contrast of the image.

First it applies a threshold on the input data, to generate a binary image. Second it labels all the coherent islands with distinct "labels".

Convolutes the input data with the user defined filter function (kernel).

Sets the intensity values outside a user-defined range either to 0 or the range values.

Is used to pick labels with the mouse and generates a binary mask.

Loads mrc stacks with default file extension .mrc in little endian byte ordering.

Writes mrc files with default file extension .mrc.

Is used to visualize molecules at positions defined in the motive-list. Additionally molecules can be selected or removed and a new motive-list can be generated.

Is used to visualize high resolved molecules at given positions in a tomogram without upsampling the tomogram or downsampling the molecules.

Computes a 2D projection from a 3D image under given angles or the given camera position.

Is used to generate photorealistic images with shadows and reflections (raytracing).

Reduces the number of pixels by a factor of 2 in all dimensions.

Rotates the input data by the given Euler angles, according to the TOM-package conventions.

Is used to calculate the rotation difference between two objects.

Loads spider files with default file extension .spi in big endian byte ordering.

Writes spider files with default file extension .spi.

Edge and Skeletonization filter. Useful for visualizing flow-like structures.

The module is only available in the Linux version.

Applies the watershed segmentation to the input data.