In fluorescence, software is key
The webiste is currently under construction.
The current state of the community
Fluorescence microscopy and spectroscopy are widely used to study biological processes on the cellular and molecular scale in real time, and provide key insights towards building a spatial, temporal and logical model of the cell as a whole. While many labs are equipped with state-of-the-art fluorescence microscopes, quantitative analysis of the acquired data often involves the use of complex algorithms and methodologies that are not easily implemented. Despite the free availability of many software packages, data analysis thus remains challenging. In our view, this situation caused by the following issues:
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Keeping up with the newest method developments is difficult due to fragmented and non-standardized software development.
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Interfacing between different software packages is cumbersome due to the lack of agreed-upon exchange file formats, making it difficult to implement custom workflows involving multiple sofwares.
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Custom implementations of published algorithms are also rarely benchmarked and tested independently, making the assessment of the validity of reported results difficult.
Our vision
We plan to bring the fluorescence software community together to provide:
- newcomers an overview of existing software packages, their use cases and contact information for active developers, and a forum to ask questions or request features.
- software developers a platform to present their software packages and discuss problems with other developers.
Moreover, we aim to:
- Increase the compatibility of existing software packages through common file exchange formats and interfaces.
- Increase the trustworthyness of algorithms through quality control and common standards.
Our vision is to provide the fluorescence microscopist and spectroscopist a bag of Legos that he or she can assemble into a custom workflow with minimal effort.
software
Improving the quality of scientific software
Data analysis and processing software is essential for an expanding fluorescence community. To improve the quality of the existing fluorescence software and to ensure that software can be used by a wide userbase, the following points have to be addressed:
- Documentation
- Correctness, Testing
- Impact and distribution
- Usability & interoperability
We aim to first gather information on existing software, classify the software and the software packages, assess the status of the software, and finally publish a curated list of the software packages as a reference for the community.
1. Gather information
Gather the software used in the fluorescence community.
2. Classify software
Software packages will be classified by:
- Their application (e.g. imaging, single-molecule spectroscopy,…)
- Programming languange used
- Open- or closed-source
3. Assess software and development status
- Contact core developers of actively developed software
- Identify the status of the software development: ongoing, finished, or abandoned
4. Publish
- interoperable software collection
- open accessible software
- Publish list of software
Developing data exchange formats
To improve on data exchange formats, we will:
- collect information on existing software
- identify interfacing points in the analysis for the different use-cases
- propose a list of needed exchange formats
register
Register
We already identified a fair amount of existing software. However, we don’t know all the nuiances of the software used in your lab. Hence, for a complete list,
We need your input!
- Please check if the software you use is listed in the software list.
- If not, register unlisted software using the registration form below.
participate
Participate
There are many ways you can contribute to our cause.
The easiest is to
Spread the word
- Tell your collegues and friends about this action.
- Use your network, e.g., Twitter, Facebook, Email to spread the news.
- Encourage your students to provide feedback to software developers
- As developer, register your software to broaden your audience.
Develop jointly
- Once you registered your software package, add it to our collection at GitHub to discuss it with other developers.