Open topic with navigation

File formats supported

Format File extension Vendor Single (S) or multi-plane (M) Read/Write Supported by Biolucida Comments
FlashPix .fpx   S R    
JPEG 2000 .jp2 JPEG S RW √

Very good quality/compression tradeoff.

Supports many channels at high bit depth.
JPEG 2000 .jpx JPEG M RW √

Multiple JP2 planes in a single file.

MBF uses an extended (but standard) version of this format to contain multiple virtual image planes and channels in a single image file.
Nanozoomer

.ndpi,.vms,

.vmu

 Hamamatsu S R √  
SVS .svs Aperio S R √ Aperio-specific format for virtual slides.
Pyramidal file format .pff Zoomify S R   Used by Zoomify viewer.
XMP Sidecar .xmp Adobe/MBF M RW   File containing lens scaling and channel information associated with a virtual slide, single image or image stack.
Format File extension Vendor Single (S) or multi-plane (M) Read/Write Supported by Biolucida Comments
Fluoview .tif, .tiff Olympus M R √ Image capture data IS embedded in the tiff tags, using standard TIFF format.

DICOM

ANALYZE

BIORAD

.dcm

.img

.pic

 Standard M R   Container format for medical imaging that can contain multiple images in various image formats.
Leica .lif Leica M R   Proprietary format for Leica microscopy imaging systems.
Nikon .ics, .ids Nikon M R    
Original Imaging Format .oif Olympus M R √ Multi-file format that includes an .oif directory containing images, lookup tables, regions of interest and scaling information.
Olympus Image Binary .oib Olympus M R √ Single binary file format that is a container for TIFF files and associated lens information for an acquired image stack.
Laser Scanning Microscopes (LSM) .lsm Zeiss M R √ Image stack format used by Zeiss microscope systems.
Zeiss Vision Image (ZVI) .zvi Zeiss M R √ Image format used by the Zeiss AxioVision for image stacks.
Format File extension Vendor Single (S) or multi-plane (M) Virtual Read/Write Supported by Biolucida Comments
Bitmap .bmp Microsoft S   RW   Microsoft's default 2D image format (MS Paint, etc.).
JPEG .jpg, .jpeg, .jpf, .mjc JPEG S   RW √ 2D - suitable for photo compression but generates artifacts for line compression.
MCID .im Interfocus Imaging S   R   Supported by MBF Bioscience Densita.
Portable Image File .pgm, .pbm, .ppm open S   R   Very simple image format with raw pixel data as a very small header.
PCX - Personal Computer Exchange .pcx ZSoft S   R  

Rarely used.

Was the native file format for PC Paintbrush.
Portable Network Graphics .png standard S   RW  

Suitable for exporting images to be used on the web.

Was created as a replacement for GIF format to avoid GIF's proprietary format's issues.
RGBA .rgba, .rgb, .bw, .sgi   S      

32-bit image format.

RGBA stands for red,green,blue, alpha channels.
Targa .tga Truevision S   R  

Rarely used.

Raster file format matching NTSC and PAL video formats.
TIFF .tif, .tiff Adobe M √ RW √ Preserves image data in non-compressed format. Limited to supporting files up to 4GB.
Format File extension Vendor Used by Read/Write Supported by Neurolucida Comments
Model data .dat MBF Neurolucida/Stereo Investigator RW   Binary format containing the modeling data for Neurolucida (dendrites, axons, somas, markers, spines) and for Stereo Investigator (probes, markers).
Model data .xml MBF Neurolucida/Stereo Investigator RW √

XML (extensible markup language) version of the .dat modeling data file.

This format contain some extensions for 3D mesh modeling not stored in the .asc and .dat file versions.
Model data .asc MBF Neurolucida/Stereo Investigator RW   Text version of the .dat modeling data file.
Model data .nrx MBF Neurolucida Explorer RW   Written by Neurolucida; read by Neurolucida Explorer.
Wavefront object .obj Wavefront 3D Visualization W   Use to export data to be used in other third-party application for 3D rendering (such as Blender)
VRML .vrml   3D Visualization W   Virtual Reality Markup Language - use to export data for 3D display in web pages.
Movie .avi   3D Visualization W   Export movies in this format for inclusion in MS Powerpoint presentations.