What is the ATF file format?
An .atf file is the standard text-based data exchange format for GenePix microarray analysis software, originally developed by Axon Instruments and now maintained by Molecular Devices (acquired 2004). It stores fluorescence intensity measurements, spot annotations, and experimental metadata from DNA microarray scans.
The format is plain tab-delimited text with a structured header block. The first line always contains ATF as its first token, followed by a literal tab separator and the version number 1.0 - the only version in widespread use. The second line declares the count of optional header lines and the number of data columns. Key=value metadata lines follow (scan settings, operator, wavelengths), then a column-name row, and finally one tab-delimited data row per microarray spot.
Two named subtypes share the ATF container:
- GPR (.GPR) - GenePix Results: per-spot fluorescence quantification data from a scanner run
- GAL (
.gal) - GenePix Array List: array layout and probe identity definitions
Both are ATF files; the Type= header field distinguishes them. Because the format is plain text with labeled columns, it opens directly in any spreadsheet application. In bioinformatics pipelines, the R limma package and the Bioconductor ecosystem read ATF/GPR files directly for microarray differential expression analysis.
Security & safety
RISK: LOWATF is plain text with no executable content. No malware risk from the format itself. Files come from microarray scanners or bioinformatics pipelines in laboratory settings.
Format details
in a nutshell- Adobe Photoshop Transfer Function - Some references cite .atf as an Adobe Photoshop internal transfer function file, but this is extremely rare and undocumented; no significant user traffic.
Programs that open ATF files
Windows3 apps
Microsoft Excel
Paid Open > select the .atf; use Text Import Wizard, choose Tab delimiter. Header lines will be included as rows. 
Notepad
Open-source Open the file directly to inspect raw text, header fields, and column structure. 
macOS2 apps
Linux2 apps
R / Bioconductor (limma package)
Open-source Use read.maimages(files, source='genepix') to load GPR/ATF files into a limma EListRaw object. Technical details
deep spec| Encoding | Plain text, ASCII/UTF-8 |
| Delimiter | Tab (\t) separating all fields |
| File signature | First line: ATF[TAB]1.0 - literal tab-separated tokens; no binary magic bytes |
| Header structure | Line 2 declares count of optional header lines and count of data columns; key=value metadata lines follow |
| Data format | One tab-delimited row per microarray spot, preceded by a column-name header row |
| Typical file size | 50 KB - 50 MB (GPR result files can be large with thousands of spots) |
| Common subtypes | GPR (GenePix Results, spot fluorescence data) and GAL (GenePix Array List, array layout) |
| Subtype identification | Type= field in the optional header block identifies subtype (GPR, GAL, or custom) |
| Associated OS | Windows, Linux, macOS (cross-platform plain text) |
| Bioinformatics integration | Read natively by the R limma package (Bioconductor) for microarray differential expression analysis |
| Developer lineage | Axon Instruments → Molecular Devices (acquired 2004); software distributed by Molecular Devices |
| Released | late 1990s (Axon Instruments GenePix software era) |
| Latest version | ATF 1.0 (current; version declared in first line) |
| Specification | support.moleculardevices.com |
ATF conversions
Community Q&A
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