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Typical data sets may have following relationships between attributes and sizes.

Volume Voxels Size (char) Size (int)
643 262,144 0.25 MB 1 MB
1283 2,097,152 2.00 MB 8 MB
2563 16,777,216 16.00 MB 64 MB
5123 134,217,728 128.00 MB 512 MB
10243 1,073,741,824 1,024.00 MB 4096 MB

Load data

In this subsection, loading methods for three data categories, single data file, stack of images and raw data set, are being introduced.

Single data file

Loading single dataset is straightforward, simply select Open->Data from the File menu, as indicated in screenshot below.

Open data

Image stacks

Loading image stacks takes a little bit more efforts than loading single data file. After selecting Open->Stack from the File menu, check all the images you would like to include in the pop-up window, as indicated in screenshots below.

Open stack

Open stack dialog

Time Series

Loading a time series is straightforward. Simply select Open->Time Series from the File menu, and select a list of files to load. Each file is considered to be one step in the time series. For more information about editing, analyzing, and visualizing time series data, see Time Series.

Reading a raw file

Users can also choose to read raw files by defining data dimensions, type, endianness, and etc, as indicated below.

Open data

HDF5 Formats

HDF5 Subsampling

Tomviz utilizes the hyperslab selection features of HDF5, so that HDF5 files may be read with subsampling.

After opening any kind of HDF5 file (includes EMD, Data Exchange, or any generic HDF5 file), the data may be reloaded and resampled by right-clicking the original dataset in the pipeline and selecting "Reload and Resample", as shown below.

Reload and Resample Context Menu

A dialog will then appear which allows the user to specify volume bounds and a stride (applied to all three axes). The dialog also conveniently provides an estimated memory usage of the dataset at the bottom.

HDF5 Subsample Dialog

Once accepted, the dataset will immediately reload with the new subsample settings.

The subsample dialog will also appear if a user attempts to open a very large HDF5 dataset, so that the user may subsample the dataset before the initial reading.


Tomviz supports reading and writing both volumes and tilt series with the EMD format. For tilt series datasets, Tomviz expects the first axis to define the angles.

As an extension of the EMD format, Tomviz also supports writing multiple scalar arrays and reading them back in. The active scalar is always written as the "data" dataset in the EMD data group. All other scalars are written by name in a "tomviz_scalars" group in the EMD data group.

Data Exchange

Tomviz supports reading volumes from Scientific Data Exchange format files.

When opening an HDF5 file, Tomviz will check to see if a dataset exists in the path "/exchange/data". If it does, the dataset will be loaded into Tomviz as a volume.

Volumes in Tomviz that are saved as a generic HDF5 file will be written in the Data Exchange format.

Generic HDF5 File

If an HDF5 file is opened that does not appear to be a format Tomviz recognizes, Tomviz will locate all three-dimensional datasets in the file. If only one three-dimensional dataset exists, Tomviz will load that dataset as a volume. If more than one exists, a dialog will appear asking the user to choose a dataset to load.

Merging Data

If two or more data sources with identical dimensions are loaded into tomviz, the user may merge them together to create either a multi-array data source, or a multi-component data source.

This is done by selecting all of the data sources that should be merged, and then right-clicking one of them to display the context menu.

Merge data context menu

Selecting to merge the data results in a dialog to indicate whether to merge the images as arrays or as components:

Merge data select

If the images are merged as arrays, one array can be viewed at a time by changing the "Active Scalars" in the properties panel.

If the images are merged as components, the components will be visualized simultaneously. In the volume module, this is done by displaying the magnitude of the components. Additionally, 3-component data can be mapped to RGB channels in the volume module.

Save results

Save data

Users can save the data by either clicking the Save Data button from File (as shown below), or simply using the keyboard short-cut Ctrl+S.

Save data

Save state

Similarly to saving data, users can save the state by clicking the Save State As button from File.

Save state as

Once a state file has been saved or loaded, Save State can be used to overwrite the same state file. For more information about the types of state files, see here.

State files

Two types of state files are available in tomviz:

  1. Full state files (.tvh5 files)
  2. Light state files (.tvsm files)

The full state files save both the state of the program and the data into a single file, which is in HDF5 format. Both input and output data are saved in the file, so that pipelines do not need to be re-ran when the file is opened.

The light state files only save the state of the program, and they use relative file paths on the file system to load the input data. When a light state file is loaded, all of the pipelines are re-ran to produce the output data.

Full state files are useful for moving the tomviz state between file systems and computers. Light state files are useful for saving progress on a single computer.

Recover and load state

Recover state

Tomviz saves the pipeline every five minutes, users can recover the previous states by simply allowing the Tomviz to load them.

Recover state

Load state

When there is no prompt, users can manually load and recover previous states by selecting Load State from File.

Load state

Both full state files and light state files may be loaded from this menu. Once a state file has been loaded, it may be overwritten via Save State. For more information about the types of state files, see here.

Exporting Data

Resulting data can be exported via many ways, which includes saving data to standard formats; taking screenshots or animations of the render view; creating an interactive scene for web browsers; exporting geometry for 3D printing and generating images of slices.

Save data

Saving data can be accessed via File menu, simply click on Save Data. Alternatively users can also simply press Ctrl+S.

Save menu

In the pop-up window, choose one of the standard formats that you want to save your data as.

Data formats

We recommend EMD (HDF5 based) for saving data. Because it supports all the data types that are used in Tomviz, and can save units in all three dimensions. However, note that it may not be as widely supported.

Besides EMD, TIFF is often the most diverse type to export to. Although it supports limited types that are used in Tomviz due to limited support for units and dimensions, it is open and widely supported by many other packages.