Still under construction…
OpenScan is a Micro-Manager -based, fully flexible and extensible open source laser scanning microscopy (LSM) platform that features composable scanning and detection routines for various LSM hardware configurations, multiple imaging modalities, and integration of data acquisition and hardware-accelerated real-time image processing.
Purpose
Laser scanning microscopy (LSM) has become a mainstay tool for biological research. Most existing LSM systems belong to one of two extremes: commercial turn-key systems that are powerful and user-friendly, but could be expensive, difficult, or even impossible to customize for a particular hardware and functionality requirement; and home-built systems either modified from commercial confocal microscopes or custom-built with off-the-shelf or custom hardware components, which give the microscopist full control but require significant effort to build, maintain, and modify. Nevertheless, both of these types of systems lack the flexibility desired by advanced microscopists and developers of new microscopy techniques.
To this end, a number of open source LSM software packages have been developed and some of these have been widely distributed outside the originating lab. However, these systems are not generally extensible but usually single-purpose, i.e., focusing on LSM features while mostly limited to particular hardware with little or no provisions for extension to additional functionalities or other imaging modalities and/or lacking the facilities to connect with a truly flexible and extensible platform for data visualization and analysis.
As such, there is an unmet need for an open source LSM system with the following features: ability to potentially support any LSM hardware, modular software framework that decouples specific hardware control from acquisition methods, standard control hardware implementation that will itself be modular and open to extension, ability to coordinate acquisition at a higher level with peripheral devices, and integration with ImageJ to enable real-time (as well as offline) analysis and visualization of image data using the solid framework and enormous selection of plugin tools developed by the biological imaging community. While many of these capabilities do exist in isolation, architecting an integrated solution is a genuine technical challenge.
On the other hand, Micro-Manager, an open source software platform for control of microscopes, has been widely adopted in the microscopy community (>10,000 installed systems), due to its free availability and more importantly its support for combinations of various hardware (>150 scientific devices) and its strong extensibility/customizability/programmability/interoperability unmatched by commercial software. Despite the vast popularity of Micro-Manager, to date, it has been missing a major imaging modality, i.e., laser scanning microscopy.
Similar to the rationale for developing Micro-Manager based open source microscopy tools such as OpenSPIM, we developed a Micro-Manager based open source LSM platform, OpenScan, to address the aforementioned challenges.
Features
OpenScan provides a flexible and open software platform that allows basic LSM functionalities to be set up with little effort, while allowing the user to assemble a different collection of components to meet the requirements of a particular experiment, either by choosing from the composable LSM modules provided by OpenScan itself, or by developing custom extensions in a quick and structured manner, or by coordinating acquisition at a higher level with other microscope devices through Micro-Manager (for example, Micro-Manager already supports photomanipulation techniques via devices such as spatial light modulators that could be used to add FRAP and photoactivation functionalities to the OpenScan based confocal imaging).
In addition to modular software, the scan control and acquisition hardware for LSM is also flexible. Besides a cost-effective, easy-to-deploy DAQ-based open-source solution, OpenScan also includes an open-source FPGA implementation for LSM control, acquisition, and on-board real-time image processing, giving advanced users the ability to fully customize all aspects of the hardware system down to the level of timing signals and DAC/ADC control, which are otherwise non-reconfigurable in traditional DAQ devices. The highly precise timing signals also enable the synchronization of LSM with other imaging modalities, e.g., FLIM, OCT, etc..
The customizability of both the FPGA code and the control software means not only that microscopists will have a platform upon which to build new microscopy techniques, but also that the LSM community will have a platform on which to share and disseminate those techniques between labs, possibly using different hardware components that conventionally are difficult to be integrated by either commercial or lab-built systems.
OpenScan is also designed to be a system with true flexibility in both acquisition and image analysis, by taking full advantage of ImageJ (with which Micro-Manager has been integrated from the beginning).
Contributors
| Bing Dai |
| Mark Tsuchida |
| Bin Li |
| Rui Xu |
| Md Abdul Kader Sagar |
| Xiaoyang Gong |
| Adib Keikhosravi |
| Michael Pinkert |
| Jenu Chacko |
Downloads
Source code
License and disclaimer
Release notes
Instructions
Hardware configuration
DAQ-based LSM system
FGPA-based LSM system
FLIM etc..
Software setup
Software setup for OpenScan developers
Programming guide