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1. Smooth Path Planning for Continuum Arms

   https://doi.org/10.1109/ICRA48506.2021.9560982  

   Meng, Brandon H. ; Godage, Isuru S. ; Kanj, Iyad ( May 2021 , IEEE International Conference on Robotics and Automation (ICRA))

   Continuum arms, with their mix of compliance, payload, safety, and manipulability, are perfectly suited to serve as co-robots, and their applications range from industry and manufacturing to human healthcare. Their hyper-redundancy serves as their most significant challenge for path planning and path planning approaches commonly used with rigid-link robots, such as inverse kinematics, that fail to provide reliable trajectories for continuum arms. We propose an Inverse Kinematics-based approach to address the limitations of previously-proposed Kinematics-based approaches. Using this new approach, we are able to efficiently generate very rich sets of configurations, which, in turn, lead to smooth path planning for such continuum manipulators. To validate the smoothness of the paths generated by our approach, we apply dynamics constraints to the generated trajectories. We show that, when tracked by a controller, the paths that are generated using the proposed approach are much smoother than previously-proposed Kinematics-based approaches: The proposed approach allows the continuum arm to traverse the trajectories very accurately and in time less than half of that taken by previous (reliable) path planning approaches. 

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2. Manipulating deformable objects by interleaving prediction, planning, and control

   https://doi.org/10.1177/0278364920918299  

   McConachie, Dale ; Dobson, Andrew ; Ruan, Mengyao ; Berenson, Dmitry ( July 2020 , The International Journal of Robotics Research)

   null (Ed.)

   We present a framework for deformable object manipulation that interleaves planning and control, enabling complex manipulation tasks without relying on high-fidelity modeling or simulation. The key question we address is when should we use planning and when should we use control to achieve the task? Planners are designed to find paths through complex configuration spaces, but for highly underactuated systems, such as deformable objects, achieving a specific configuration is very difficult even with high-fidelity models. Conversely, controllers can be designed to achieve specific configurations, but they can be trapped in undesirable local minima owing to obstacles. Our approach consists of three components: (1) a global motion planner to generate gross motion of the deformable object; (2) a local controller for refinement of the configuration of the deformable object; and (3) a novel deadlock prediction algorithm to determine when to use planning versus control. By separating planning from control we are able to use different representations of the deformable object, reducing overall complexity and enabling efficient computation of motion. We provide a detailed proof of probabilistic completeness for our planner, which is valid despite the fact that our system is underactuated and we do not have a steering function. We then demonstrate that our framework is able to successfully perform several manipulation tasks with rope and cloth in simulation, which cannot be performed using either our controller or planner alone. These experiments suggest that our planner can generate paths efficiently, taking under a second on average to find a feasible path in three out of four scenarios. We also show that our framework is effective on a 16-degree-of-freedom physical robot, where reachability and dual-arm constraints make the planning more difficult. 

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3. Stampede: A Discrete-Optimization Method for Solving Pathwise-Inverse Kinematics

   Rakita, Daniel ; Mutlu, Bilge ( May 2019 , 2019 International Conference on Robotics and Automation (ICRA))

   We present a discrete-optimization technique for finding feasible robot arm trajectories that pass through provided 6-DOF Cartesian-space end-effector paths with high accuracy, a problem called pathwise-inverse kinematics. The output from our method consists of a path function of joint-angles that best follows the provided end-effector path function, given some definition of ``best''. Our method, called Stampede, casts the robot motion translation problem as a discrete-space graph-search problem where the nodes in the graph are individually solved for using non-linear optimization; framing the problem in such a way gives rise to a well-structured graph that affords an effective best path calculation using an efficient dynamic-programming algorithm. We present techniques for sampling configuration space, such as diversity sampling and adaptive sampling, to construct the search-space in the graph. Through an evaluation, we show that our approach performs well in finding smooth, feasible, collision-free robot motions that match the input end-effector trace with very high accuracy, while alternative approaches, such as a state-of-the-art per-frame inverse kinematics solver and a global non-linear trajectory-optimization approach, performed unfavorably. 

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4. Hardness of Motion Planning with Obstacle Uncertainty in Two Dimensions

   https://doi.org/10.1177/0278364921992787  

   Shimanuki, Luke ; Axelrod, Brian ( September 2021 , The International Journal of Robotics Research)

   We consider the problem of motion planning in the presence of uncertain obstacles, modeled as polytopes with Gaussian-distributed faces (PGDFs). A number of practical algorithms exist for motion planning in the presence of known obstacles by constructing a graph in configuration space, then efficiently searching the graph to find a collision-free path. We show that such an exact algorithm is unlikely to be practical in the domain with uncertain obstacles. In particular, we show that safe 2D motion planning among PGDF obstacles is [Formula: see text]-hard with respect to the number of obstacles, and remains [Formula: see text]-hard after being restricted to a graph. Our reduction is based on a path encoding of MAXQHORNSAT and uses the risk of collision with an obstacle to encode variable assignments and literal satisfactions. This implies that, unlike in the known case, planning under uncertainty is hard, even when given a graph containing the solution. We further show by reduction from [Formula: see text]-SAT that both safe 3D motion planning among PGDF obstacles and the related minimum constraint removal problem remain [Formula: see text]-hard even when restricted to cases where each obstacle overlaps with at most a constant number of other obstacles. 

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5. Recent Advances in the Temple University Digital Pathology Corpus

   https://doi.org/10.1109/SPMB47826.2019.9037859  

   Hunt, I. ; Husain, S. ; Simon, J. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad ; Picone, Joseph ; Selesnick, Ivan (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing a large open source database of high-resolution digital pathology images known as the Temple University Digital Pathology Corpus (TUDP) [1]. Our long-term goal is to release one million images. We expect to release the first 100,000 image corpus by December 2020. The data is being acquired at the Department of Pathology at Temple University Hospital (TUH) using a Leica Biosystems Aperio AT2 scanner [2] and consists entirely of clinical pathology images. More information about the data and the project can be found in Shawki et al. [3]. We currently have a National Science Foundation (NSF) planning grant [4] to explore how best the community can leverage this resource. One goal of this poster presentation is to stimulate community-wide discussions about this project and determine how this valuable resource can best meet the needs of the public. The computing infrastructure required to support this database is extensive [5] and includes two HIPAA-secure computer networks, dual petabyte file servers, and Aperio’s eSlide Manager (eSM) software [6]. We currently have digitized over 50,000 slides from 2,846 patients and 2,942 clinical cases. There is an average of 12.4 slides per patient and 10.5 slides per case with one report per case. The data is organized by tissue type as shown below: Filenames: tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_0a001_00123456_lvl0001_s000.svs tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_00123456.docx Explanation: tudp: root directory of the corpus v1.0.0: version number of the release svs: the image data type gastro: the type of tissue 000001: six-digit sequence number used to control directory complexity 00123456: 8-digit patient MRN 2015_03_05: the date the specimen was captured 0s15_12345: the clinical case name 0s15_12345_0a001_00123456_lvl0001_s000.svs: the actual image filename consisting of a repeat of the case name, a site code (e.g., 0a001), the type and depth of the cut (e.g., lvl0001) and a token number (e.g., s000) 0s15_12345_00123456.docx: the filename for the corresponding case report We currently recognize fifteen tissue types in the first installment of the corpus. The raw image data is stored in Aperio’s “.svs” format, which is a multi-layered compressed JPEG format [3,7]. Pathology reports containing a summary of how a pathologist interpreted the slide are also provided in a flat text file format. A more complete summary of the demographics of this pilot corpus will be presented at the conference. Another goal of this poster presentation is to share our experiences with the larger community since many of these details have not been adequately documented in scientific publications. There are quite a few obstacles in collecting this data that have slowed down the process and need to be discussed publicly. Our backlog of slides dates back to 1997, meaning there are a lot that need to be sifted through and discarded for peeling or cracking. Additionally, during scanning a slide can get stuck, stalling a scan session for hours, resulting in a significant loss of productivity. Over the past two years, we have accumulated significant experience with how to scan a diverse inventory of slides using the Aperio AT2 high-volume scanner. We have been working closely with the vendor to resolve many problems associated with the use of this scanner for research purposes. This scanning project began in January of 2018 when the scanner was first installed. The scanning process was slow at first since there was a learning curve with how the scanner worked and how to obtain samples from the hospital. From its start date until May of 2019 ~20,000 slides we scanned. In the past 6 months from May to November we have tripled that number and how hold ~60,000 slides in our database. This dramatic increase in productivity was due to additional undergraduate staff members and an emphasis on efficient workflow. The Aperio AT2 scans 400 slides a day, requiring at least eight hours of scan time. The efficiency of these scans can vary greatly. When our team first started, approximately 5% of slides failed the scanning process due to focal point errors. We have been able to reduce that to 1% through a variety of means: (1) best practices regarding daily and monthly recalibrations, (2) tweaking the software such as the tissue finder parameter settings, and (3) experience with how to clean and prep slides so they scan properly. Nevertheless, this is not a completely automated process, making it very difficult to reach our production targets. With a staff of three undergraduate workers spending a total of 30 hours per week, we find it difficult to scan more than 2,000 slides per week using a single scanner (400 slides per night x 5 nights per week). The main limitation in achieving this level of production is the lack of a completely automated scanning process, it takes a couple of hours to sort, clean and load slides. We have streamlined all other aspects of the workflow required to database the scanned slides so that there are no additional bottlenecks. To bridge the gap between hospital operations and research, we are using Aperio’s eSM software. Our goal is to provide pathologists access to high quality digital images of their patients’ slides. eSM is a secure website that holds the images with their metadata labels, patient report, and path to where the image is located on our file server. Although eSM includes significant infrastructure to import slides into the database using barcodes, TUH does not currently support barcode use. Therefore, we manage the data using a mixture of Python scripts and manual import functions available in eSM. The database and associated tools are based on proprietary formats developed by Aperio, making this another important point of community-wide discussion on how best to disseminate such information. Our near-term goal for the TUDP Corpus is to release 100,000 slides by December 2020. We hope to continue data collection over the next decade until we reach one million slides. We are creating two pilot corpora using the first 50,000 slides we have collected. The first corpus consists of 500 slides with a marker stain and another 500 without it. This set was designed to let people debug their basic deep learning processing flow on these high-resolution images. We discuss our preliminary experiments on this corpus and the challenges in processing these high-resolution images using deep learning in [3]. We are able to achieve a mean sensitivity of 99.0% for slides with pen marks, and 98.9% for slides without marks, using a multistage deep learning algorithm. While this dataset was very useful in initial debugging, we are in the midst of creating a new, more challenging pilot corpus using actual tissue samples annotated by experts. The task will be to detect ductal carcinoma (DCIS) or invasive breast cancer tissue. There will be approximately 1,000 images per class in this corpus. Based on the number of features annotated, we can train on a two class problem of DCIS or benign, or increase the difficulty by increasing the classes to include DCIS, benign, stroma, pink tissue, non-neoplastic etc. Those interested in the corpus or in participating in community-wide discussions should join our listserv, nedc_tuh_dpath@googlegroups.com, to be kept informed of the latest developments in this project. You can learn more from our project website: https://www.isip.piconepress.com/projects/nsf_dpath. 

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