How to Export RDML Files from Bio-Rad CFX Maestro Software

To export an RDML file from Bio-Rad CFX Maestro, open your run file (.pcrd), go to File > Export > RDML, choose your save location, and click Save. The exported .rdml file contains your raw fluorescence data, well setup, sample names, and Cq values — everything a downstream analysis tool needs to work with your data. That's the short version.

The longer version matters because CFX Maestro has gone through several iterations, Bio-Rad has changed where they put the export options, and there are a few settings that affect what actually ends up in your RDML file. If you've ever exported what you thought was a complete file only to find your sample names missing or your well assignments blank, this post covers why that happens and how to avoid it.

What's in an RDML File (and Why You'd Want One)

RDML (Real-time PCR Data Markup Language) is an open XML-based standard for exchanging qPCR data between instruments and software platforms. It was developed by the RDML consortium (Lefever et al., 2009) specifically because every instrument manufacturer uses a proprietary file format — Bio-Rad uses .pcrd, Applied Biosystems uses .eds, Roche uses .ixo — and none of them talk to each other.

An RDML file from CFX Maestro typically contains:

• Raw fluorescence readings for every cycle of every well
• Well assignments: sample names, target/gene names, sample types (unknown, standard, NTC, positive control)
• Cq (Ct) values as calculated by the instrument software
• Baseline and threshold settings used for Cq determination
• Melt curve data if you ran a dissociation step

What it does not contain is the thermal cycling protocol itself (ramp rates, hold times) or any post-run analysis like relative quantification or gene expression ratios. That's fine — those are things you should be doing in dedicated analysis software anyway, not in the instrument's built-in tools.

Step-by-Step Export from CFX Maestro 2.0 and Later

Bio-Rad released CFX Maestro 2.0 as a significant overhaul of their software interface. If you're running a CFX96, CFX96 Touch, CFX Connect, or CFX Opus, and your software was installed or updated after roughly 2020, you're almost certainly on 2.0 or later (current version as of this writing is 2.3).

Here's the exact workflow:

1. Open your run file. Launch CFX Maestro and open the .pcrd file for the run you want to export. You can do this from the Start tab or File > Open > Data File.

2. Verify your plate setup. Before exporting, click the Plate tab and confirm that your sample names, target names, and sample types are correctly assigned. This is the single most common source of problems — if you ran the plate using a "quick plate" setup without entering sample names, those fields will be blank in the RDML export. You can edit the plate setup retroactively from this tab; just make sure to click Apply when done.

3. Go to File > Export > Export RDML File. In some sub-versions this is under File > Export > RDML (.rdml). Either way, a dialog box will appear letting you choose a filename and save location.

4. Choose what to include. CFX Maestro 2.0+ gives you a checkbox option to include or exclude Cq values in the export. Leave this checked unless you have a specific reason not to (for instance, if you plan to re-call Cq values in external software using different baseline settings).

5. Click Save. Your .rdml file is now ready.

One thing to note: CFX Maestro also offers an Export to Spreadsheet option, which gives you a .csv or .xlsx file. That's not the same as RDML. The spreadsheet export is tab-delimited data that's readable in Excel but doesn't carry the structured metadata that analysis tools expect. If a downstream tool asks for RDML, give it RDML.

Exporting from CFX Maestro 1.1 (Legacy)

If you're on an older machine running CFX Maestro 1.1 or even the older CFX Manager (version 3.x), the export path is slightly different:

1. Open your .pcrd file.
2. Navigate to File > Export and look for the RDML option. In CFX Manager 3.1, this is listed as Export > RDML (v1.1) or RDML (v1.2) — choose v1.2 if your downstream software supports it, as it carries more metadata.
3. If you don't see an RDML export option at all, your software version may be too old. CFX Manager versions prior to 3.0 had limited or no RDML support. You'll need to update the software (free from Bio-Rad's website with a valid instrument serial number) or export as .csv and work with that instead.

One frustrating quirk of CFX Manager 3.x: it sometimes exports RDML files where the fluorescence data is present but the Cq values are missing, particularly if you modified the threshold or baseline settings after the initial analysis. Re-analyzing the data (Quantification > Analyze) before exporting usually fixes this.

Common Problems and How to Fix Them

Blank sample names in the exported file. This happens when you set up the run using a quick plate or a protocol-only setup and never entered sample and target names. Fix it by editing the plate setup in CFX Maestro before exporting. Open the Plate tab, enter your names, apply changes, then export.

"No data" errors when importing the RDML into another tool. Some third-party tools expect RDML v1.3 or later. CFX Maestro 2.0+ exports RDML v1.2 by default. Most modern analysis platforms handle v1.2 fine, but if yours doesn't, you may need to convert the file using the RDML-Linker tool available at rdml.org.

Melt curve data missing. If your protocol included a melt step but the RDML file doesn't seem to contain melt data, check whether you're looking in the right place. RDML stores amplification data and melt data in separate sections. Some importing tools only read the amplification section by default.

File won't open / corrupt file. RDML files are just zipped XML. If you're troubleshooting, rename the .rdml extension to .zip, unzip it, and look at the XML inside. The main data file is usually called rdml_data.xml. If this file is truncated or empty, the export was interrupted — re-export from CFX Maestro.

Multiple fluorophore channels. If you ran a multiplex experiment (say, a FAM-labeled target and a HEX-labeled reference), the RDML file will contain data for all channels. Make sure the target names are assigned to the correct fluorophores in your plate setup before exporting, or you'll spend 20 minutes untangling which channel is which in your analysis software.

A Note on RDML Versions

The RDML standard has gone through several versions: 1.0, 1.1, 1.2, 1.3, and 1.4. The differences mostly relate to how much metadata can be stored (experiment descriptions, annotation fields, digital PCR support in 1.3+). For standard qPCR data — amplification curves, Cq values, sample/target setup — version 1.2 covers everything you need, and that's what CFX Maestro exports.

If you're working with a tool that specifically requires a newer version, the RDML consortium provides converters at rdml.org. In practice, I've rarely encountered a situation where the version mismatch actually caused a problem with qPCR data — it's more relevant for dPCR workflows.

Batch Exporting Multiple Runs

CFX Maestro doesn't offer a built-in batch export for RDML files. If you have 15 runs from a time-course experiment and you need RDML files for all of them, you're opening each .pcrd file individually and exporting one at a time. It's tedious but unavoidable within the software itself.

If you find yourself doing this regularly, a practical workaround is to script it. The .pcrd files are essentially SQLite databases (you can verify this by opening one in a hex editor — the header starts with SQLite format 3). Several open-source tools, including the Python python-rdml library maintained by the RDML consortium, can read .pcrd files directly and convert them to RDML programmatically. This requires some comfort with Python, but if you're processing dozens of runs, it saves real time.

Alternatively, VoilaPCR accepts RDML files directly and handles the parsing, plate layout reconstruction, and Cq extraction automatically — so once you've got your files exported, the analysis side is taken care of without manual reformatting.

Practical Takeaway

Export RDML from CFX Maestro before you close the run file, right after you've verified your plate setup looks correct. It takes ten seconds and gives you a portable, instrument-independent copy of your data. Your future self — or your collaborator on a different instrument platform — will thank you.