SPLASSH: Open source software for camera-based high-speed, multispectral in-vivo optical image acquisition

Abstract

Camera-based in-vivo optical imaging can provide detailed images of living tissue that reveal structure, function, and disease. High-speed, high resolution imaging can reveal dynamic events such as changes in blood flow and responses to stimulation. Despite these benefits, commercially available scientific cameras rarely include software that is suitable for in-vivo imaging applications, making this highly versatile form of optical imaging challenging and time-consuming to implement. To address this issue, we have developed a novel, open-source software package to control high-speed, multispectral optical imaging systems. The software integrates a number of modular functions through a custom graphical user interface (GUI) and provides extensive control over a wide range of inexpensive IEEE 1394 Firewire cameras. Multispectral illumination can be incorporated through the use of off-the-shelf light emitting diodes which the software synchronizes to image acquisition via a programmed microcontroller, allowing arbitrary high-speed illumination sequences. The complete software suite is available for free download. Here we describe the software’s framework and provide details to guide users with development of this and similar software.

Emerging Business Models for Open Source Hardware

“…The Arduino platform has been used for many scientific applications including: lowcost UAVs for oceanographic research (Busquets, et al, 2012), behavioral experiments (D'Ausilio, 2012), pressure monitoring (Russell et al, 2012), drop velocity measurements (Fobel, et al, 2013), microscopy (Gualda, et al, 2013), electrophysiology (Newman, et al, 2012), Skinner boxes (Pineño, 2014), and multi-spectral in-vivo optical image acquisition (Sun et al, 2010). In addition, the Ardunio-enabled RepRap has been modified to work as a printed circuit board (PCB) mill (Anzalone, et al, 2015), so that the Arduino main board itself can be fabricated using the RepRap along with a wide range of Open Source circuit designs.…”

Low-Cost Open-Source Voltage and Current Monitor for Gas Metal Arc Weld 3D Printing

“…For example, they have been used for oceanographic research [13], mass spectrometry [14,15], microscopy [16], vision research [17], Skinner boxes [18], mechatronics [19], optics [10,20], electrophoresis [21], and imaging [22,23]. Most importantly for this sensor application, Arduinos have applied to systems for sensors for open hardware [24] including colorimetry [25], nephelometry [26], pressure monitoring [27], smart plugs [28], and in vivo optimal imaging [29]. In addition, Arduinos have been demonstrated for field sensing operations like soil moisture [30], developing a wireless sensor node to monitor poultry farms [31] and an ambient sensor cloud system using OpenFS (open field server) for high-throughput phenotyping [32].…”

An inexpensive Arduino-based LED stimulator system for vision research

“…Arduino has been employed in scientific applications such as LED light control of an open-source in vivo multispectral imaging system for rodents (Sun et al, 2010), teaching violin bowing by providing an interface for combining motion sensing and vibrotactile feedback (van der Linden et al, 2011), smart textile design with optical fiber integration to clothes (Parkova et al, 2011), wearable computing (Buechley and Eisenberg, 2008;Isoyama et al, 2011), and in cross-disciplinary teaching of biology and computer science (Grasel et al, 2010).…”