Open Source Microscopy Software

University Of California, San Francisco, San Francisco CA

Investigators

Linked publications & trials

Abstract

DESCRIPTION (provided by applicant): Ever since the inception of the microscope by van Leeuwenhoek in the 17th century, microscopy has been the cornerstone technology of biological sciences. Today, digital microscopy is revolutionizing basic life science and clinical research. Direct observation through an eyepiece is becoming uncommon and is rapidly being replaced by data collection using digital cameras. In addition to a digital camera, contemporary microscopes have several motion devices (shutters, motorized states, filter wheels or turrets, z-drives, etc.) whose operation needs to be orchestrated according to the researcher's experimental needs. Thus, software control of microscope image acquisition has become indispensable. There are several commercial software packages available, but they suffer from 1) limitations in the hardware they can control, 2) impossibility of adding hardware support to change their hardwired experimental strategies, 3) the 'black box'syndrome, i.e. the tendency to make it difficult to work together with other software and databases, and 4) high cost. To remedy this situation, we have developed Open Source Software that controls microscope image acquisition. The software is easy to install and operate, yet can be extended at any level. For instance, hardware support can be added by the end-user and experimental strategies can be changed using a built-in scripting language. The user interface has been shaped with extensive help of researchers in the lab. The software is maintained on multiple platforms (Windows, Mac, Linux). Here, we aim to extend our initial software by greatly increasing the number of supported hardware and by enabling high speed and multi-position acquisition. We plan to make it easier for researchers to change the software by adding automatic code generation and strengthening the existing scripting facilities. We also propose adding features needed to drive automated, high -throughput microscopes and to integrate the software with databases and analysis environments. Through these and additional improvements, we expect that this software (provided free of charge) will ultimately be used in at least 5,000 microscope workstations worldwide. With Open Source software, researchers also will be able to more easily execute creative, novel imaging strategies. Narrative: This project will result in flexible, extendible software that researchers will use to operate light microscopes. The software will be freely available, and will not only make possible novel experimental approaches, but also make digital microscopy much more accessible to researchers world-wide.