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Using SIS Converter

Setting the preferences

From the main dialog, select Preferences.
The Preferences dialog opens.

Tick the boxes of the options you want selected. Click on the boxes again to deselect them.
Finish setting the preferences by clicking OK.

The following preferences are available:

Importing channel colors

If enabled and supported by the corresponding media handler, color settings are transferred from the source file to the SIS file.

If disabled, or enabled and not supported by the corresponding media handler, no special color settings are applied to the SIS file.

The default color settings are as following:

Color range according to bit depth:

8bit: 0 - 255

16bit: 0 - 65535

32bit float: 0 - 1

Channel colors according to the number of channels:

One channel: Gradient from black to white

Two channels: Channel 1: Gradient from black to red / Channel 2: Gradient from black to green

Three channels: Channel 1: Gradient from black to red / Channel 2: Gradient from black to green / Channel 3: Gradient from black to blue

More than three channels: The first three channels are the same as the three channels above. All other channels are the same as one channel.

Disable blending

(OFF by default)

Enable this option, if you don't need blending on the tile borders, for example when you sliced a big image into smaller tiles for easier transfer.

Disabling this option ensures that tiled input files have smooth tile borders after the import is finished.

Using GZIP compression

(ON by default)

If enabled, image data will be compressed without loss of information to reduce the file size.

This is especially useful for environments with limited disk space or transfer bandwidth. The compression rate depends on the image content.

Creating Restore Point

(ON by default)

Enabling this option will create a restore point right after the import process is finished. Using this option enables you to revert any changes to the state after the import and before any changes were made.

Importing files

To import images, choose Add Files... from the main menu, or drag and drop files or folders onto an open arivis SIS Converter window. You will be guided through the import process and be able to work with your data after the import process finishes.
The selected files are analyzed and, depending on the number and structure of the input files, a dialog box appears.
If your import file is a single, simple image file, the following Import files dialog box is displayed:

The imported file will be located at the displayed location.
To change the destination file, modify the path manually or use the Browse button to display a file save dialog.
Click on more options to change the Target Pixel Type or Show file information.

Importing complex or multiple input files

If your input file is complex, or you wish to import multiple input files, different scenarios are suggested in the Import files dialog:

The imported file will be located at the displayed location.

To change the destination file, modify the path manually or use the Browse button.
A file save dialog will be displayed.
Click on more options to change the Target Pixel Type or Show file information.

Modifying the list of files

Open the Detailed file information dialog, which can be found under more options in every import dialog box, to modify the list of files for your import scenario.
Remove files from the import list and freely change the order in which the input files are imported.

Complex Import

To import complex, unknown, image structures, select the Custom Import scenario.

It enables you to freely define your import scenario in detail. If the suggested scenarios do not fit your need, this dialog is your partner in defining your import scenario.

Manual import mapper

The Manual import mapper displays a table with information about what regions of the input files are mapped to what regions in the destination file. Initially, each channel of the input data is specifically mapped to the destination file and will be presented as one line in the mapping table.

For a large number of files, the Manual Mapper approach is not suitable.

The Selection menu provides you with easy-to-use wizards to perform different tasks in order to create custom mappings. Before accessing a specific wizard, please mark all lines inside the mapping table that you want to change. You can press CTRL-A to mark all input files at once.

Pattern matching

Sometimes the filenames contain information that define on which dimension each image has to be located in the resulting image.

Choose Selection > Pattern matching... to open the import pattern matching dialog. Here you can define a pattern that contains specific identifiers that mark parts of the input filename as a locator for an image dimension.
The identifiers match numeric values (including leading zeros). Use the wildcard identifiers * and ? to ignore other numeric values. If your input files start counting a dimension at 100, Edit offsets helps you set a new start for counting. E.g. if your first input file is named "input_plane0100_frame010_channel01", and you don't adjust the offsets, your resulting file may contain empty data. To alleviate this change the plane offset to -100, the time point offset to -10, and the channel offset to -1. Now your resulting file will only contain the data you set up to import.
Press the Refresh button to refresh the preview of how the current pattern affects your import scenario in the lower preview panel.

Supported image formats

arivis SIS Converter supports a large number of image formats. Media handlers are extension plug-ins which enable arivis SIS Converter to import and export files in various file formats. For instance, the importers and exporters use these media handlers.

The following media-handlers are available in your arivis SIS Converter:

Amira-Mesh Media Handler

The Amira-Mesh media handler enables the import of Amira-Mesh files, containing uniform lattice data. Amira-Mesh files can contain different types of data, for instance spatial graphs or stacked lattices. This media handler is not able to read these special data types.

The Amira-Mesh media handler allows you to import images of the following file format: Amira-Mesh (*.am)

The DeltaVision media handler

The DeltaVision media handler enables the import of Applied Precision's DeltaVision image files.

The DeltaVision media handler allows you to import images of the following file format: DeltaVision (*.dv)

Dicom Media Handler

The Dicom media handler enables arivis SIS Converter to read DICOM containers or DICOMDIR files. These files describe the structure of a DICOM dataset (Digital Imaging and Communications in Medicine) that is most commonly used in medical working areas.

The Dicom media handler allows you to import images in the following file formats: Dicom (*.dcm) , DICOMDIR (*.dicomdir)

Hamamatsu Media Handler

The Hamamatsu media handler allows you to import images of the following file format: NDPI (*.ndpi) , Virtual Microscope Specimen (*.vms)

ICS Media Handler

The ICS media handler allows you to import images of the following file format: ICS 1.0 (*.ics) , ICS 2.0 (*.ids)

Imaris Media Handler

The Imaris media handler enables the import of the Bitplane Imaris file format (IMS). The Imaris media handler is using the HDF5 Library.

JPEG Media Handler

The JPEG media handler enables an optimized import of JPEG image files.

It allows you to import images of the following file format: JPEG (*.jpg, *.jpeg)

Mirax Media Handler

The Mirax media handler enables the import of the Mirax SlideAC file format. This image format originates from Carl Zeiss Mirax Slide scanner systems and is based on image pyramids.

The Mirax media handler allows you to import images of the following file format: Mirax SlideAC (*.mrxs)

NIfTI Media Handler

The NIfTI media handler enables the import of the NIfTI (Neuroimaging Informatics Technology Initiative) image file formats.

The NIfTI media handler allows you to import images of the following file formats: single-file(combined data and meta- data)(.nii) ,single-file gzip-compressed (.nii.gz) , dual- file(separate data and meta-data, respectively)(.img/.hdr)

RAWInfo Media Handler

The RAWInfo media handler enables the import of raw image files by using a control (*.rawinfo) file that contains dimension information.

The Raw media handler allows you to import images of the following file formats: RawInfo (*.rawinfo)

Slide Book Media Handler

The Slide Book media handler enables the import of the Slide Book file format.

The Slide Book media handler allows you to import images in the following file format: Slide Book (*.sld)

Tiff Media Handler

The Tiff media handler enables the import of TIFF (Tagged Image File Format) based image file formats. TIFF is a commonly used format to store images.

The Tiff media handler allows you to import images of the following file formats: TIFF (*.tif, *.tiff) , OME TIFF (*.tif, *.tiff)

VOL Media Handler

The VOL media handler enables the import of VG Studio VOL images.

The VOL media handler allows you to import images of the following file format: VOL (*.vol/*.vgi)

To import a VG Studio VOL dataset both files (.vol & .vgi) are needed!