OpenWSI: a low-cost, high-throughput whole slide imaging system via single-frame autofocusing and open-source hardware

Abstract

Recent advancements in whole slide imaging (WSI) have moved pathology closer to digital practice. Existing systems require precise mechanical control and the cost is prohibitive for most individual pathologists. Here we report a low-cost and high-throughput WSI system termed OpenWSI. The reported system is built using off-the-shelf components including a programmable LED array, a photographic lens, and a low-cost computer numerical control (CNC) router. Different from conventional WSI platforms, our system performs real-time single-frame autofocusing using color-multiplexed illumination. For axial positioning control, we perform coarse adjustment using the CNC router and precise adjustment using the ultrasonic motor ring in the photographic lens. By using a 20X objective lens, we show that the OpenWSI system has a resolution of ~0.7 µm. It can acquire whole slide images of a 225-mm 2 region in ~2 mins, with throughput comparable to existing high-end platforms. The reported system offers a turnkey solution to transform the highend WSI platforms into one that can be made broadly available and utilizable without loss of capacity. OCIS codes: (170.0180) Microscopy; (170.4730) Optical pathology; (120.4570) Optical design of instrumentsDigital pathology via whole slide imaging (WSI) promises better and faster diagnosis and prognosis of cancers and other diseases [1]. A major milestone was accomplished in 2017 when the Philips' WSI system was approved for the primary diagnostic use in the US [2]. In a conventional WSI system, the tissue slide is mechanically scanned to different x-y positions and the digital images are acquired using a high numerical aperture (NA) objective lens. The small depth of field of the objective, however, poses a challenge for proper focusing during the scanning process [3,4]. Many existing systems create a focus map prior to the scanning process. For each point on the map, the system needs to scan the sample to different axial positions and acquire a z-stack. The best focus position can then be inferred based on the image with the highest Brenner gradient or other figure of merits [5][6][7]. In this z-stack approach, surveying the focus points for every tile would require a prohibitive amount of time. Most systems select a subset of tiles for focus point surveying to save time. Different from the z-stack approach, we have recently demonstrated a focus map surveying method based on singleframe autofocusing [8,9]. In this approach, we illuminate the sample from two different incident angles. If the object is placed at an out-offocus position, the captured image would contain two copies of the object separated by a certain distance. The defocus distance can then be recovered based on the two-copy separation.In this letter, we report the development of a low-cost, highthroughput DIY WSI system termed OpenWSI. The reported system is built using off-the-shelf components including a programmable LED array, a photographic lens, and a low-cost computer numerical control (CNC) router. Different from con...

Autofocusing technologies for whole slide imaging and automated microscopy

“…Dual-LED illumination has recently been demonstrated for single-frame autofocusing while the sample is in continuous motion [134][135][136][137][138]. Figure 10A shows one of the reported configurations where two near-infrared LEDs F I G U R E 1 0 Dual-LED illumination for single-frame autofocusing.…”

“…This dual-LED scheme has also been demonstrated for focus map surveying with only one main camera [136]. Figure 10B1 shows a further development of the dual-LED approach using color multiplexed illumination [137,138]. In this scheme, a color LED array is used for sample illumination.…”

“…If the sample is placed at an out-of-focus position, the red and the green copy will be separated by a certain distance, as shown in the insets of Figure 10B1. One can then identify the translational shift of the redand green-channel images by maximizing the image mutual information or cross-correlation [137,138]. The resulting translational shift is used for dynamic focus correction in the scanning process.…”

“…The resulting translational shift is used for dynamic focus correction in the scanning process. Figure 10B2 shows an open-source WSI platform, termed OpenWSI, based on the color-multiplexed dual-LED autofocusing scheme [138]. This OpenWSI platform is built with low-cost, off-the-shelf components including a programmable LED array, a photographic lens and a F I G U R E 1 1 Deep learning approaches for autofocusing.…”

Simple Shading Correction Method for Brightfield Whole Slide Imaging

“…Whole slide imaging (WSI), which refers to scanning a whole slide and creating a single high-resolution digital image, is a relatively new technique that solves the narrow field of view (FOV) problem of traditional optical microscopes [1][2][3]. Since the introduction of the automated WSI device in 1999 [4], the WSI devices can acquire faster and more accurate high-quality digital images of the whole slide due to its recent advances in hardware and software technologies [1,5]. These advances have made it possible for pathologists to convert from viewing slides from a microscope to a computer monitor that displays high-resolution whole-slide images [3].…”