CDF File

What are CDF files and how to open them

Are you having problems opening a CDF file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your CDF files.

What is a CDF file?

CDF files have multiple uses, and Affymetrix Chip Definition is one of them. Read more about the other uses further down the page.

Affymetrix Chip Definition File

A Chip Definition File created by Affymetrix defines how a GeneChip microarray is built and how to interpret its raw data. It describes which physical spots ("cells" or "probe cells") belong to which logical probe sets that typically represent genes or genomic features. It is not generated by experiments; instead, Affymetrix or its users produce it for each chip type so that downstream software can map raw cell intensities (in CEL files) to biological meaning.

The file is used as a reference: one file per microarray design. It includes the geometry of the array (number of rows and columns), all probe sets ("units"), and for each probe set the membership information of its probes ("atoms" or "cells"), which are individual physical probes. Everything - from whether probes are sense or anti-sense, groups of cells ("blocks" or "groups"), perfect match/mismatch probes, probe-target base position, and other metadata - is defined. Software for microarray analysis uses the CDF to interpret experimental signal data properly.

Internally this format exists in at least two versions: a text-based version and a binary version called "XDA". In the text version the file is arranged in sections named [CDF], [Chip], [UnitJ] and [UnitJ_BlockK]. Tags like Version, Rows, Cols, NumberOfUnits appear. In the block definitions there are tags like CellHeader followed by fields such as X, Y, PROBE, FEAT, QUAL, EXPOS, POS, CBASE, PBASE, TBASE, ATOM, INDEX and others. The file begins with a signature "[CDF]" at offset zero and contains many recognizable strings such as UNIT1000_BLOCK1, NUMBEROFUNITS, NUMBERCELLS, among others.

How to open CDF files

Important: Different programs may use files with the CDF file extension for different purposes, so unless you are sure which format your CDF file is, you may need to try a few different programs.

While we have not verified the apps ourselves yet, our users have suggested ten different CDF openers which you will find listed below.

Last updated: August 31, 2026

All known file formats using extension .CDF

While Affymetrix Chip Definition File is a popular type of CDF-file, we know of 5 different uses of the .CDF file extension. Different software may use files with the same extension for different types of data.

Channel Definition Format File

We know that one CDF format is Channel Definition Format File. We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

Common Data Format

Common Data Format (version 2.5 or earlier) holds scientific data and metadata in a self-describing, discipline- and platform-independent structure. It is used to store multidimensional arrays (called variables) along with descriptive information about them (attributes), so that data and its meaning travel together. The format supports both scalar and n-dimensional data, allows metadata about the whole dataset or individual variables, and ensures portability between different systems. It is primarily produced and managed through NASA's Space Physics Data Facility, originally by the National Space Science Data Center. Version 2.5 is the official variant used by the ISTP (International Solar‐Terrestrial Physics) project.

Variables in this format may be of types including scalars, vectors, or arrays with arbitrary dimensions. Metadata entries (attributes) describe units, valid ranges, names, dimensions, pad values etc., either for specific variables or globally. Data encoding choices (host, network/XDR, or machine-specific formats), record‐ vs. single-file layouts, and interfaces in C and Fortran allow users to read/write data and metadata via standard or internal APIs. CDF files created in or before version 2.5 remain readable by later library versions through backward compatibility.

The file begins with a CDF Descriptor Record ("CDR") containing fields such as version, release, and increment. For example, "version" and "release" are stored as signed 4-byte integers at offsets 20 and 24 in the header. The format also includes fixed-positions for encoding and flags, and uses embedded metadata strings such as "FORMAT", "SPACE PHYSICS", "SUPPORT". Keywords in descriptors include rVariables and zVariables, and attributes (g/rEntries, zEntries). Certain reserved fields ("Copyright", "Encoding", "Flags", etc.) are also part of the header.

Computable Document Format File

The Computable Document Format File is a document authored in Wolfram's Computable Document Format standard, designed to capture interactive content - such as text, graphics, calculations, typeset mathematics, and UI elements - and make them usable without full Mathematica software. It is created by Wolfram products (including Mathematica or Wolfram's cloud authoring tools), and it is intended for distribution so that readers can interact with its dynamic elements using free or otherwise limited viewers like Wolfram Player. It combines aspects of an app and a document so that readers can live-drive content (for example by manipulating sliders or buttons or viewing automatic computations).

Files in this format are produced when a creator saves a notebook or interactive resource as a CDF through Mathematica or related Wolfram development tools. They are then read by Wolfram Player, Wolfram Player Pro, or Mathematica itself. Depending on licensing (for example "FreeCDF" vs. "EnterpriseCDF") some runtime restrictions apply in viewers: enterprise or paid versions allow fuller interactivity while free viewers may limit certain elements like some non-numeric inputs or external data import/export.

CDF files are text-based using Wolfram Language expression syntax (structured like Mathematica notebooks). They are cross-platform and usually readable in text editors: they start with a Content-type header identifying them as Wolfram CDF text documents.

Byte signatures include a header beginning with "( Content-type: application/vnd.wolfram.cdf.text )" at the very start of the file (offset zero), which identifies it uniquely as a Wolfram Computable Document Format File.

NetCDF Network Common Data Form

NetCDF Network Common Data Form is a file format designed for storing scientific data in arrays - often multidimensional grids like time-series, latitude-longitude grids, or 3D models of atmosphere or ocean. It is especially used for research in Earth sciences, climate modeling, meteorology, oceanography and geospatial analyses. The format allows data values and detailed metadata (such as units, coordinate systems, variable names and attributes) to be saved together, making the file "self-describing."

Files in this format are created by software built on the netCDF library, maintained by Unidata, which provides APIs in languages such as C, Fortran, C++, and Java. Those libraries also read and write the files. Common workflows include scientific data generation, sharing datasets for modeling or observations, and using the files as input for visualization or further scientific computation. Data are stored in named dimensions and variables, with optional "unlimited" dimensions for appending records.

There are several variants of the format: classic format (also called CDF-1), 64-bit offset format (CDF-2), 64-bit data format (CDF-5), and netCDF-4 which uses an HDF5 backend supporting enhanced features. Each variant defines how large datasets, offsets, and metadata are represented. Files support portability across different machine architectures via external representation standards.

Files using this format begin with an ASCII signature in their header: the first four bytes are "C", "D", "F", followed by a version byte (for example \x01 for classic CDF-1, \x02 for CDF-2, \x05 for CDF-5). Other header data includes the number of records, list of dimensions, list of global (and variable) attributes, list of variables, and then the data arrays themselves.

Various apps that use files with this extension

These apps are known to open certain types of CDF files. Remember, different programs may use CDF files for different purposes, so you may need to try out a few of them to be able to open your specific file.

Help us help others

File.org helps thousands of users every day, and we would love to hear from you if you have additional information about CDF file formats, example files, or compatible programs. Please use the links below or email us at submit@file.org to discuss further.