Supported File Formats
The following list describes the supported file formats.
Image Formats
The following list describes the supported image file formats.
| Format | Description | Import | Export |
|---|---|---|---|
| TIFF (*.tif, *.tiff) | One of the most widely supported lossless compression file formats for storing bit-mapped images for both PCs and Macintosh computers, Tagged Image File Format (TIFF) files can be uncompressed or LZW compressed. | Yes | Yes |
| TXM (*.txm, *.txrm)* | File format used by ZEISS Xradia 3D X-ray microscopes. | Yes | No |
| CZI (*.czi)* | File format used by ZEISS microscopes. | Yes | Yes |
| JPEG (*.jpg, *.jpeg, *.jpe) | A standard format that stores images in a compressed form. The JPG format is lossy compressed according to a quality value, which can range from 100 — the highest quality, but also the largest file size — down to 1, which creates a poor quality, small file. JPG lossy compression can lead to artifacts that may not be compatible with quantitative analyzes. | Yes | Yes** |
| JPEG 2000 (*.jp2) | The lossy JPEG 2000 file format can provide better compression performance with improved image quality compared to the original JPEG file format. A higher dynamic range is also supported by this format, with no limit to image bit depth. | Yes | No |
| PNG (*.png) | The Portable Network Graphics (PNG) format is a more powerful alternative to the GIF file format. PNGs are stored in compressed form using a lossless compression algorithm. The format is also able to store an alpha channel. | Yes | Yes** |
| Bitmap (*.bmp, *.dib) | BMP… Standard uncompressed bit-mapped graphics format used in Windows.
DIB… A device independent Windows-defined image format that stores data for each pixel in the image without any compression. The main purpose of device independent bitmaps (DIBs) is to allow bitmaps to be moved from one device to another, in contrast to a Windows’ device-dependent BMPs. |
Yes | Yes** |
| RAW (*.raw and *.pic) | Saves images as raw pixel data without a header. Suitable for transferring files between applications and computer platforms. Header information is saved in an accompanying DAT file when RAW files are saved in Dragonfly. | Yes | Yes |
| DAT (*.dat) |
Header file for referenced RAW data. An example DAT file is:
ObjectFileName… FileName.raw
|
Yes | Yes |
| Analyze 7.5 (*.hdr) | The Analyze file format was developed at the Mayo Clinic as part of a software package of the same name. Datasets in this format consist of small HDR files that describe the data and IMG files with the raw data. Although there are multiple versions of this format, Dragonfly only supports the 7.5 variant. | Yes | Yes |
| NIfTI (*.nii) | A file format for the exchange of neuro imaging data. NIfTI data objects can consist of two files, an HDR file containing the header information and an IMG file which contains the raw image data. A dedicated file extension NII is also available for storing the header and the data in the same file. | Yes | No |
| REK (*.rek) | Fraunhofer EZRT volume data file. | Yes | No |
| MRC (*.mrc) | A file format for electron density that has become an industry standard in cryo-electron microscopy. It was developed by the MRC (Medical Research Council) Laboratory of Molecular Biology. | Yes | Yes |
| Volumeinfo (*.volumeinfo) |
Text file saved by Comet Xylon CT systems for referenced raw data that provides the settings needed to open the RAW file correctly. Information contained in the file includes: Size (in pixels)… Provides the size of the volume in the X, Y, and Z axes. Data type… Indicates the numeric data type — unsigned/signed char, unsigned/signed short, unsigned/signed int, float — in which the raw data was saved. Image spacing… Indicates the voxel size in the X, Y, and Z axes. Offset… Is the offset that is applied to the histogram which shifts its values – offsets it – by some amount. In this case, the output is computed as [(input) + (offset)]. Slope… Changes the slope of the transfer function without shifting the black level established by the offset value. This controls the contrast of an image and is computed as [(input) ´ (slope)]. |
Yes | No |
| Dragonfly Object (*.ORSObject and *.xml) | Theset files are proprietary binary formatted files in which data is written sequentially and XML (Extensible Markup Language) is appended after the binary data. This file format can also be used to save regions of interest, multi-ROIs, and other objects. | Yes | Yes |
| Avizo/Amira (*.am) | General purpose file format for Thermo Fisher Scientific's Avizo and Amira applications. Dragonfly only supports structured grids saved in the AM file format. | Yes | No |
| Digital Micrograph (*.dm4) | File format for Digital Micrograph, which is an image processing program produced commercially by Gatan. Note Refer to https://personal.ntu.edu.sg/cbb/info/dmformat/index.html#dm4 for more information about the DM4 file format. |
Yes | No |
| NetCDF (*.nc) | NetCDF (network Common Data Form) is a file format for storing multidimensional scientific data (variables), such as temperature, humidity, pressure, wind speed, and direction. Each of these variables can be displayed through a dimension. | Yes | No |
| DICOM (*.dcm) | Standard file format for medical images. Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging. It includes a file format definition and a network communications protocol. | Yes | Yes |
| Scanco (*.aim) | File format associated with microCT systems developed by SCANCO Medical AG. | Yes | No |
| VFF (*.vff) | Modified version of the (now defunct) SunVision volume file format. VFF files have a plain text header that describes image dimensions, voxel sizes, origin, offset, and scale factor. | Yes | No |
| Vox (*.vox) | MagicaVoxel file format, which is a free, lightweight 8-bit voxel editor. | Yes | No |
| VTK (*.vtk) | File format used by the Visualization Toolkit, which is an open-source software system for 3D computer graphics, image processing, and scientific visualization. | Yes | Yes |
* Available for Dragonfly 3D World ZEISS edition only. Contact Comet Technologies Canada for information about the availability of this version of Dragonfly.
** Available for 8 bit images only.
Unstructured Grid (Mesh) Formats
The following list describes the supported unstructured grid (mesh) file formats.
| Description | Import | Export | |
|---|---|---|---|
| 3D Studio Max (*.3ds) | 3DS is one of the file formats used by the Autodesk 3ds Max 3D modeling, animation, and rendering software and has become a de facto industry standard for transferring models between 3D programs, or for storing models for 3D resource catalogs. | Yes | No |
| BREP (*.brep and *.rle) | The Boundary Representation file format is used to store 3D models that can consist of vertices, edges, wires, faces, shells, solids, compounds, edge triangulations, face triangulations, polylines on triangulations, space location and orientation. ASCII encoding is used to read and write to the BREP format. | Yes | No |
| CSFDB (*.csfdb and *.csf) | Open CASCADE 3D Model file. | Yes | No |
| DirectX (*.x) | DirectX files that define 3D geometries. | Yes | No |
| OBJ (*.obj) |
Generic 3D file format that contains geometry descriptions.
Note Dragonfly does not support the import of associated MTL files, which are written in a proprietary format. Only the mesh geometries, not materials nor textures, can be imported for this format. |
Yes | Yes |
| PLY (*.ply) | The PLY format was developed at Stanford for storing points and geometries. When writing to this format, additional information such as vertex colors and scalar values will included. | Yes | Yes |
| STL (*.stl and *.dib) | Stereo Lithography (STL) files are widely used as a standard for rapid prototyping applications. Most computer-aided design (CAD) applications provide an STL output format, which was developed by 3D Systems. | Yes | Yes |
| VRML (*.wrl) | Virtual Reality Modeling Language (VRML) files are ASCII text files with VRML tags. VRML is a subset of the Silicon Graphics Open Inventor file format and is used for storing 3D geometries. | Yes | Yes |
| VTK Polydata (*.vtk) | Generic Visualization Toolkit (VTK) data file format. | Yes | Yes |
| VTK Polydata XML (*.vtp) | Generic Visualization Toolkit (VTK) data file format. | Yes | Yes |
| VTK Unstructured Grid (*.vtk) | Generic Visualization Toolkit (VTK) unstructured grid file format. | Yes | No |
| MESH (*.mesh) | Native file format of Medit, a program for visualizing scientific models. | Yes | Yes |
| Dragonfly Object (*.ORSObject) | Dragonfly Object files are proprietary binary formatted files in which data is written sequentially and XML (Extensible Markup Language) is appended after the binary data. Meshes saved in this format will retain their scalar values. | Yes | Yes |
