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Using SIS Converter

Opening the arivis SIS Converter

Execute arivis SIS Converter by clicking on the related icon on the desktop.
The arivis SIS Converter dialog opens.

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.

More options

Save Folder: This option sets the default folder for any file you wish to import. It is still possible to change the folder on a case by case basis.

Custom Directory: Sets the directory to save the output file in to a folder of your choice.

Source Directory: Sets the directory to save the output file in to the folder of the input file.

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.

Apply dimension order

By applying dimension templates to your input files, you can easily define how your images are arranged in the different dimensions which the internal image model provides. If you have, for example, input files for two channels that should be organized as a result dataset with 10 time points and 20 planes, you can configure the dimension order as shown in the following screenshot:

Arranging the order of the template elements

The order of the template elements defines in which order your input files are arranged dimensionally. Setting the time point dimension to a value of 5 means: Take every 5th image and add it to a new time point.

Press Add Dimension to add a new selector to the current template.
Click Remove to remove an element.
Click Up or Down to change the order of the dimensions.
Press Update preview to display a preview of how the current template affects your import scenario in the lower preview panel.
To apply the current template and change your current mapping, press OK.

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)

Aperio Media Handler

The Aperio media handler allows you to import images of the following file format: Aperio (JPEG) (*.svs) , Aperio JPEG2000) (*.svs)

Metamorph Media Handler

The Metamorph media handler is part of the Bio Media Handler Module which enables the import of some common image formats used in biology-related working areas.

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

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)

Hamamatsu Media Handler

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

FreeImage Media Handler

The FreeImage media handler enables the import for most of the common image formats.

It allows you to import images of the following file formats:

JPEG / JFIF (*.jpg;*.jpeg;*.jif;*.jfif;*.j;*.jpe) TIFF Tagged Image (*.tif;*.tim;*.tiff)
Windows Bitmap (*.bmp;*.rle;*.vga;*.rl4;*.rl8;*.sys) Portable Network Graphics (*.png)
CompuServe GIF (*.gif;*.giff)
JPEG-2000 (*.jp2)
High Dynamic Range Image (*.hdr)

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)

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)

Leica Media Handler

The Leica media handler enables the import of Leica image file formats.

The Leica media handler allows you to import images of the following file formats: Leica Image File Format (*.lif) , Leica LCS (*.lei)

LSM Media Handler

The LSM media handler enables the import of the LSM file formats.

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)

Nikon Media Handler

The Nikon media handler enables the import of data created by the Nikon imaging solutions.

The Nikon media handler allows you to import images of the following file format: Nikon ND2 (*.nd2)

Olympus Media Handler

The Olympus media handler enables the import of the Olympus OIB/OIF file formats.

The Olympus media handler allows you to import images of the following file formats: Olympus OIB (*.oib) , Olympus OIF (*.oif)

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)

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!