What is the GPR file format?
A .gpr file is the raw results output of a GenePix laser microarray scanner, produced by GenePix Pro software from Molecular Devices (formerly Axon Instruments). It stores fluorescence intensity measurements for every spot on a DNA or protein microarray slide, supplying the primary quantitative data for downstream differential expression analysis.
The format is based on ATF (Axon Text Format): a plain-text, tab-delimited structure readable in any text editor or spreadsheet. The first line always reads ATF followed by a tab and the version string 1.0. An optional block of key-value header records follows, then a tab-delimited column-header row, and finally the data rows - one per microarray spot.
Each data row contains the spot's grid coordinates (Block, Row, Column), an annotation identifier, and approximately 60-100 fluorescence metrics per channel. For a standard two-color experiment the channels are typically Cy3 at 532 nm and Cy5 at 635 nm, reported as median and mean foreground and background intensities along with quality flags and morphology scores (Circularity, SNR).
.gpr files are commonly used alongside .gal files (GenePix Array List), which supply spot name and ID annotations. Downstream analysis is typically performed in R/Bioconductor - the limma package's read.maimages() function reads .gpr natively. Raw .gpr files are accepted as supplementary data by the NCBI GEO database.
Security & safety
RISK: LOWGPR files are plain text scientific data with no executable content. They are generated by laboratory instruments and pose no malware risk. The only practical safety concern is data integrity - GPR files from external sources should be validated against the experiment's metadata and the expected number of spots to detect accidental truncation or corruption.
Format details
in a nutshell- GoPro RAW Image (GoPro GPR) - GoPro cameras (HERO5/6/7/8/9, Fusion, MAX) save 12-bit RAW photos as .gpr - a DNG extension using VC-5 lossless compression, with a separate JPG sidecar. Opened by Adobe Lightroom, Photoshop (Camera Raw 9.7+), and the open-source GoPro GPR SDK. Completely unrelated to the GenePix format.
- Finale/Sibelius music notation project (GigaStudio/Giga Performer) - Some music software versions used .gpr for project/performance files; niche and rare.
Programs that open GPR files
Windows4 apps
GenePix Pro Software
Paid File > Open GPR - the native tool for GenePix results; provides full visualization and analysis. 
Microsoft Excel
Paid Open the .gpr file (it's tab-delimited text): Data > From Text/CSV or simply rename to .txt and open. Review the ATF header rows, then work with the data table. Choose 'Tab' as delimiter. 
LibreOffice Calc
Open-source Open the .gpr - LibreOffice recognizes it as a text file and prompts for delimiter (choose Tab). Free alternative to Excel for inspecting the data table.
R / Bioconductor (limma package)
Open-source read.maimages(files, source='genepix') reads GPR files natively. The standard tool for microarray differential expression analysis. 
macOS2 apps
R / Bioconductor (limma)
Open-source Same as Windows - read.maimages() is the standard analysis path on any OS. 
Linux1 app
R / Bioconductor (limma)
Open-source The primary analysis environment for GPR data on Linux; read.maimages() handles the ATF format. Technical details
deep spec| File structure | ATF (Axon Text Format) - plain text, tab-delimited |
| Header signature | Line 1: ATF<tab>1.0; followed by optional key-value header block, then column-header row |
| Data unit | One row per microarray spot (feature), with ~60-100 numeric measurement columns |
| Primary channels | Cy3 at 532 nm and Cy5 at 635 nm (standard two-color microarray configuration) |
| Key column types | F532/F635 (foreground median/mean), B532/B635 (background), Flags, Circularity, SNR |
| Encoding | ASCII or UTF-8 plain text; no binary sections |
| ATF version | 1.0 (declared in line 1; the only version in widespread use) |
| Typical file size | 500 KB - 50 MB (scales with number of spots on the array) |
| Companion file | .gal (GenePix Array List) supplies spot name and ID annotations |
| R integration | limma::read.maimages() reads .gpr natively for differential expression analysis |
| Operating system | Windows (GenePix Pro); macOS/Linux via R/Bioconductor pipelines |
| GEO submission | Raw .gpr files accepted as supplementary data by NCBI Gene Expression Omnibus (GEO) |
| Released | late 1990s (Axon Instruments GenePix scanners; Molecular Devices acquired Axon ~2004) |
| Latest version | GenePix Pro 7 (most recent major version); ATF format version 1.0 |
| Open standard | Yes · royalty-free |
| Specification | www.cryer.co.uk |
GPR conversions
Community Q&A
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