Vratis, an image-processing software startup based in Wroclaw, Poland, is spearheading an effort to build an open-source software platform to support high-throughput biological screening.
The company, a recent spin-out of Wroclaw University of Technology, has submitted a proposal for the project, called the Open Screening Environment, to the European Union’s 7th Framework funding mechanism, Lukasz Miroslaw, CEO of Vratis, told Cell-Based Assay News.
Miroslaw said that the company has already enlisted several academic partners for the effort, including the Max Planck Institute of Cell Biology and Genetics, the Biotechnological Center of the Dresden University of Technology, and Konstanz University of Technology.
Inaugural components for the platform include the company’s own suite of open source image-analysis tools — a visualization tool called TracePilot and a 3D cell-tracking package called Cell Detective — as well as an image analysis workflow environment from MPI-CBG called BioImage and a data-mining package from the Konstanz University of Technology called KNIME (Konstanz Information Miner).
Miroslaw described these modules as “a good starting place for a larger high-throughput screening system,” and said that the company is hoping to attract additional partners in order to support “the complete screening process.”
Vratis envisions an open-source integrated platform that will eventually encompass components for screening, bioinformatics, data mining, structural genomics, image analysis, visualization, phenotyping, and genotyping, Miroslaw said.
The company is seeking partners who could “either support the idea, provide additional packages, or apply the software in biological experiments — basically to test it in screening,” Miroslaw said.
“We see that there is a gap in the market and we hope to fill it,” he added.
Building a Business on Open Source
Vratis was founded last year, but won’t launch officially until this April, Miroslaw said. The company’s founders are from Wroclaw University of Technology, MPI-CBG, and the Dresden University of Technology, where they collaborated on a number of projects to develop image-processing software for biological applications.
Last year, they decided to found a company based on the same sort of services they were providing their academic collaborators. The company name is derived from Vratislavia, the Latin name for the firm’s home town.
Miroslaw said Vratis was awarded an undisclosed amount of start-up funding when it won a business model competition organized by Wroclaw Center for Technology Transfer.
“As a consequence we got financial support from Wroclaw Technology Park and EU Structural Funds within the Integrated Regional Operational Program,” he said. The company’s founders provided additional funding, he said.
So far, TracePilot is the only package that has been publicly released. Developed as part of a collaboration with MPI-CBG to help track cells in the developing zebrafish brain in real time, the work was published last April in the journal Developmental Dynamics and is available for download under the GNU open source license here.
Tadeusz Dracz, technical advisor for Vratis, is the lead developer for TracePilot as well as other packages that are still under development, including Cell Detective, which also supports the zebrafish brain development project. Miroslaw did not provide a timeline for the launch of that package.
A third package, BioImage, will be released this month. BioImage allows users to construct workflows of different image-processing algorithms with different parameters using a drag-and-drop interface.
“Imagine that you have a set of blocks, and each represents an algorithm, and each block has its inputs and outputs, and you can combine those blocks into pipelines and try different linking combinations and at each point you can also change parameters,” Miroslaw said. “It’s a general platform to test different solutions very fast.”
Miroslaw said that the company intends to release all of its software under an open-source license, and that its business model is to provide image-processing development services based on its freely available tools, as well as those of its partners.
The BioImage package is expected to be a cornerstone for this strategy, he said, because the company anticipates that some users will require custom image-analysis modules to plug into the workflow framework, which they would hire Vratis to develop.
“We see that there is a gap in the market and we hope to fill it.”
In addition, the four-person company has developed a suite of general-purpose image-processing algorithms that it intends to license à la carte to third-party software developers.
“These methods are quite sophisticated and we believe they can be used by other companies that have their own image-processing software,” Miroslaw said.
Filling a Gap?
“To our knowledge there exists no open-source application that supports high-throughput biological screening with software capable to manage and analyze all data generated during experiments,” Vratis wrote in its FP7 proposal. “Our existing and future software solutions will fill this gap.”
There are other open source projects in the image-analysis field, however. CellProfiler, from the Broad Institute, is specifically designed for high-throughput image-based cell-screening experiments. In addition, the Open Microscopy Environment, an international open source project, is building a platform to support data management for biological light microscopy.
Miroslaw said that he sees an opportunity for OSE to coordinate its efforts with other projects in the area. In the case of OME, “they have developed a very well-defined XML [format for] describing the screening process, so we want to contact them and try to combine what they did with our solution,” he said.
“Our intention is that OSE would also stand for Open Source Environment, and we believe that if everybody could add their own components, their own modules, then maybe it will grow faster, like Linux,” he said.
Further information on the OSE project is available here.