Script Hub

Script Hub™ is your central source for C1™ methods and applications. Get access to scripts and other applications developed by Fluidigm and the C1 community, including epigenetics, mRNA sequencing, DNA sequencing, cell staining and more.

Callisto System Software v3.8.13

The latest operating system upgrade for the Callisto™ system. To install, follow the instructions found in the Callisto System User Guide (in Chapter 3, see Update the System).

Script Builder Software v2.1.1

C1™ Script Builder™ allows you to create innovative single-cell applications to deeply explore cellular heterogeneity and the functional attributes of every cell population. Download the latest version of Script Builder here, then follow the instructions for installation. Note: Script Builder can be used without a license to design custom protocols. A license is required to transform custom protocols into scripts and install them on your C1 system.

C1 System Software v2.2.3

The C1™ system supports DNA sequencing, mRNA sequencing, targeted gene expression, miRNA analysis and additional applications through the C1 Open App™ IFC (integrated fluidic circuit). Download the C1 system software update and then follow the instructions for updating the C1 system software.

MCD Viewer

MCD™ Viewer is post-acquisition data processing software that allows users to visualize, review, and export Imaging Mass Cytometry™ data acquired with the Hyperion™ Imaging System and CyTOF® Software 6.7.

Access Array FC1 Cycler Software

FC1™ Cycler software update to enable running the 48.48 Targeted DNA Sequencing Library Preparation system protocol on the Access Array™ system.

Callisto Experiment Planner v2.0.1

Easily design and create intricate multifactorial dosing, feeding and harvesting protocols for your cell modeling experiment on Callisto™. Save and share protocols with colleagues to ensure reproducible and reliable cell culture results.

Access Array Firmware and Software Update

Access Array™ firmware and software update v2.8

IFC Controllers Software (HX, MX, RX, and WX)

Copy and extract HX, MX, RX and WX folders on to a USB drive. Place the folders into the root directory of the drive. DO NOT place the folders into another subfolder or the instrument will not recognize the folder names. Follow the instructions found in the IFC Controller user guide that came with your controller.

Singular Analysis Toolset Practice Sets v3.6

Practice your Singular™ Analysis Toolset software skills with this set of sample scripts. Validate your technique before you commit valuable resources.


The histoCAT™ software is an innovative computational Imaging Mass Cytometry™ analysis toolbox that enables comprehensive analysis of cellular phenotypes and their interrelationships within the spatial context of the tissue microenvironment. Developed in the laboratory of Bernd Bodenmiller at the University of Zurich, histoCAT includes novel algorithms to identify the relationships and “social networks” between cells in healthy and disease states and across experimental cohorts. Under the agreement with the University of Zurich, Fluidigm obtained rights to globally distribute histoCAT along with the Hyperion™ Imaging System.



Biomark & EP1 Software

Data Collection Software

SNP Genotyping Analysis
Our innovative SNP Genotyping software, is designed specifically for analyzing genotyping data acquired from Biomark™ or EP1™ systems. Advanced features include cluster-calling algorithm technology, multiple IFC scoring and automatic confidence score ratings.

Real-Time PCR Analysis
Quick and efficient Real-Time PCR Analysis software helps you easily establish standard curves, calculate delta delta Ct and automatically determine the ideal threshold setting for each run. Specifically created for Biomark systems.

Digital PCR Analysis
Featuring tools specific to digital PCR, our innovative software offers real-time analysis, automated copy number variation, endpoint imaging and the ability to quantitate up to four targets per sample using multiple reporter dyes. Designed for use with Biomark and EP1 systems.

Melt Curve Analysis



Juno Software

Juno™ software update to enable running the Juno Targeted DNA Sequencing Library Preparation system protocol version 3.9.1

C1 mRNA Seq HT Demultiplex Script

The C1™ mRNA Sequencing High Throughput Demultiplexer Perl script application programming interface (API) allows automatic demultiplexing of individual single-cell samples from each column using the cell barcodes on the R1 reads. The API also automatically separates the large FASTQ file generated from each column pool into 40 pairs. This enables your C1 medium-cell HT IFC data to be preprocessed in a more efficient way.