Pathobin Product Catalogue 2018 Download a purchase order form www.pathobin.com
Pathobin 3D System... 3 Pathobin C-mount Camera... 5 Pathobin Mosaic software... 7 PathobinTools software... 9 2
Pathobin 3D System The Pathobin 3D System is the only automated 3D photogrammetry and modeling system designed specifically for pathology specimens in the world. It has been designed from the ground up using established Structure-from-Motion techniques [1-4], modified to suit anatomical pathology laboratory and specimen requirements. The Pathobin 3D System including digital turntable and user control software have been tailored to suit anatomical pathology specimens by providing: A large surface which is expandable to over 1m diameters, smoothly rotating up to 10kg specimens. A washable turntable board that can be replaced by the user with other materials (e.g. cork board, specimen mounts, foam). Interfacing with familiar DSLR camera and capture settings*. Up to 18-megapixel equivalent texture resolution. Detailed surface meshes of over 100k polygons. Fast capture time of approximately 20 seconds. Fast 3D generation time of 2 to 5 minutes**. Output to various 3D file formats including 3D PDF. Figure 1 Pathobin digital turntable and optional Canon EOS 700D 3
Figure 2 3D captured thyroid gland from point cloud to texture-mapped model in minutes. *The Pathobin user control software is designed to interface with Canon EOS cameras. A pre-configured Canon EOS 700D camera is included on request. Compatibility with other models may vary. **Performance will vary with PC speed. An Intel Core i7 CPU or equivalent with at least 8GB RAM running Windows 8 or above is recommended. References: 1. Westoby, M.J., et al., 'Structure-from-Motion' photogrammetry: A low-cost, effective tool for geoscience applications. Geomorphology, 2012. 179: p. 300-314. 2. Snavely, N., S. Seitz, and R. Szeliski, Modeling the World from Internet Photo Collections. International Journal of Computer Vision, 2008. 80(2): p. 189-210. 3. Baltsavias, E.P., et al., Digital Surface Modelling by Airborne Laser Scanning and Digital Photogrammetry for Glacier Monitoring. The Photogrammetric Record, 2001. 17(98): p. 243-273. 4. Urbanova, P., P. Hejna, and M. Jurda, Testing photogrammetry-based techniques for threedimensional surface documentation in forensic pathology. Forensic Sci Int, 2015. 250: p. 77-86 4
Pathobin C-mount Camera The Pathobin C-mount USB3.0 CMOS Camera (PBUCC-001) is an ultra-high performance microscope camera with a massive 5GB/s transfer rate ensuring a high frame rate and image quality during demanding tasks, such as real-time whole slide scanning. The Pathobin USB C-mount Camera is compatible with an included advanced video and image processing application, known as PathobinTools, as well as the Pathobin Mosaic software (see below). Features: High performance USB3.0 interface (also compatible with USB2.0 ports). No special graphic hardware or video cards required. Super fast refresh rate. Single frame resolution up to 3.1-megapixel. Compatible with Pathobin Mosaic software for whole slide scanning and image resolutions over 200-megapixels. Figure 3 The Pathobin USB C-mount Camera (PBUCC-001) with machined aluminium body and USB3.0 connection. 5
A C-mount phototube to suit various microscopes (including Olympus, Nikon and more) is also available on request. Table 1 Sensor and size Pixel (µm) FPS/Resolution Binning Exposure 3.1M 1/3 (4.51x3.38mm) 2.2x2.2 27.3@2048x1534 53.3@1024x770 1x1, 2x2 0.1ms~2000ms 6
Pathobin Mosaic software The Pathobin Mosaic software is an affordable manual whole slide scanner solution that works with the Pathobin C-mount Camera or other standard microscope cameras*, allowing a pathologist to scan a whole slide in real-time and generate a digitised whole slide image (WSI) without the need for expensive whole slide scanner machinery or proprietary software. A revolution in digital microscopy, the Pathobin Mosaic software utilizes realtime image stitching via point feature trackers, motion models and random sample consensus (RANSAC). By combining algorithms described in unmanned aerial vehicle (UAV) mapping of ground targets and illumination correction of individual frames fed from the microscope camera we are able to generate large, virtually seamless, image mosaics of well over 200 megapixels. Figure 4 These high-resolution image mosaics can be used for meetings or presentations with the potential for educational telepathology in a remote pathology setting. They may also be used for digital image analysis research projects with the ability to digitally segment regions of tumour from surrounding tissues and inflammatory cells across a large area that may not be possible from conventional microscope images. Eliminates cost barriers by avoiding the need for expensive hardware. Is easily accessible as distributable software. Reduces file sizes normally associated with WSI. May improve throughput with 10X objective equivalent and lower scans in comparison to WSI machinery. Uses standardised output formats (JPEG). Images can be uploaded to Pathobin.com and shared over a web browser through the free online Pathobin WSI zoom viewer with the option for private secure cases. 7
*The Pathobin Mosaic software requires a PC running Windows 8 or above, at least 8GB RAM and either the Pathobin C-mount USB3.0 CMOS Camera or a DirectShow compatible microscope camera (check with your microscope vendor whether they provide DirectShow drivers). References: 1. Zhou, Guoqing. "Near real-time orthorectification and mosaic of small UAV video flow for time-critical event response." IEEE Transactions on Geoscience and Remote Sensing 47.3 (2009): 739-747. 2. Kekec, Taygun, Alper Yildirim, and Mustafa Unel. "A new approach to real-time mosaicing of aerial images." Robotics and Autonomous Systems 62.12 (2014): 1755-1767. 3. Kaynig, Verena, et al. "Fully automatic stitching and distortion correction of transmission electron microscope images." Journal of structural biology 171.2 (2010): 163-173. 8
PathobinTools software The PathobinTools application is included free with every purchase of the Pathobin USB C-mount Camera and includes professional camera controls. PathobinTools provides: Exposure and Gain adjustment. o Enable automatic exposure control (with an exposure target) or choose manual exposure options. White Balance. o Advanced single-click intelligent spot white balance setting. Color Adjustment. o Hue, saturation, brightness, contrast, gamma. Anti-flicker power frequency setting. o Natural light, DC, AC 50 HZ, AC 60HZ switch functions eliminate video flicker. Flip horizontal or vertical image orientation. Skip and bin sampling. o Bin mode may obtain a lower noise video stream; Skip mode may obtain a sharper and smoother video stream. Supports a video stream histogram extension, negative and positive switching, gray calibration and clarity factor for focusing. Load and save all settings. Video functions. o Record and playback, video broadcast, time lapse capture, video watermark, video stream grid, video measurement, video calibration, gray calibration, video EDF, basic image stitching, video scale bar, date and time stamp. 9
Image Processing and Enhancement. o Control and adjust image by contrast, denoise, filtering algorithms and mathematical morphology algorithms, image rotate, scale and print. 2D Measurement. o Take measurements of area, perimeter, angle and more. Measurement results can be hierarchical controlled according to characteristics or preferences. Image Segmentation and Feature Counting. o Integrate the advanced 6 image segmentation and particle counting algorithm (Watershed (W), OTSU Dark, OTSU Bright, RGB Histogram, HSV Histogram and Color Cube) with or without a manual segmentation function (split objects) ensuring the success of image complete segmentation. The count result can be exported to Microsoft Excel for data analysis. Color Composite. o Color composite adds an appropriate pseudo-colour to monochrome fluorescence images. Fluorescence probe and color can be chosen from a pre-defined database. A dye database can also be easily created for special fluorescence probes. PathobinTools requires a PC with an Intel Core 2, 2.8GHz or higher CPU, at least 2GB RAM and a USB port. 10