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1. Analysis of shape data: From landmarks to elastic curves

   https://doi.org/10.1002/wics.1495  

   Bharath, Karthik ; Kurtek, Sebastian ( January 2020 , WIREs Computational Statistics)

   Proliferation of high‐resolution imaging data in recent years has led to substantial improvements in the two popular approaches for analyzing shapes of data objects based on landmarks and/or continuous curves. We provide an expository account of elastic shape analysis of parametric planar curves representing shapes of two‐dimensional (2D) objects by discussing its differences, and its commonalities, to the landmark‐based approach. Particular attention is accorded to the role of reparameterization of a curve, which in addition to rotation, scaling and translation, represents an important shape‐preserving transformation of a curve. The transition to the curve‐based approach moves the mathematical setting of shape analysis from finite‐dimensional non‐Euclidean spaces to infinite‐dimensional ones. We discuss some of the challenges associated with the infinite‐dimensionality of the shape space, and illustrate the use of geometry‐based methods in the computation of intrinsic statistical summaries and in the definition of statistical models on a 2D imaging dataset consisting of mouse vertebrae. We conclude with an overview of the current state‐of‐the‐art in the field.

   This article is categorized under:

    

   Image and Spatial Data < Data: Types and Structure

   Computational Mathematics < Applications of Computational Statistics

    

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2. 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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3. Debugging by design: A constructionist approach to high school students' crafting and coding of electronic textiles as failure artefacts

   https://doi.org/10.1111/bjet.13079  

   Fields, Deborah A. ; Kafai, Yasmin B. ; Morales‐Navarro, Luis ; Walker, Justice T. ( March 2021 , British Journal of Educational Technology)

   Much attention in constructionism has focused on designing tools and activities that support learners in designing fully finished and functional applications and artefacts to be shared with others. But helping students learn to debug their applications often takes on a surprisingly more instructionist stance by giving them checklists, teaching them strategies or providing them with test programmes. The idea of designing bugs for learning—ordebugging by design—makes learners agents of their own learning and, more importantly, of making and solving mistakes. In this paper, we report on our implementation of ‘Debugging by Design’ activities in a high school classroom over a period of 8 hours as part of an electronic textiles unit. Students were tasked to craft the electronic textile artefacts with problems or bugs for their peers to solve. Drawing on observations and interviews, we answer the following research questions: (1) How did students participate in making bugs for others? (2) What did students gain from designing and solving bugs for others? In the discussion, we address the opportunities and challenges that designing personally and socially meaningful failure artefacts provides for becoming objects‐to‐think‐with and objects‐to‐share‐with in student learning and promoting new directions in constructionism.

   What is already known about this topic

   There is substantial evidence for the benefits of learning programming and debugging in the context of constructing personally relevant and complex artefacts, including electronic textiles.

   Related, work on productive failure has demonstrated that providing learners with strategically difficult problems (in which they ‘fail’) equips them to better handle subsequent challenges.

   What this paper adds

   In this paper, we argue that designing bugs or ‘failure artefacts’ is as much a constructionist approach to learning as is designing fully functional artefacts.

   We consider how ‘failure artefacts’ can be both objects‐to‐learn‐with and objects‐to‐share‐with.

   We introduce the concept of ‘Debugging by Design’ (DbD) as a means to expand application of constructionism to the context of developing ‘failure artifacts’.

   Implications for practice and/or policy

   We conceptualise a new way to enable and empower students in debugging—by designing creative, multimodal buggy projects for others to solve.

   The DbD approach may support students in near‐transfer of debugging and the beginning of a more systematic approach to debugging in later projects and should be explored in other domains beyond e‐textiles.

   New studies should explore learning, design and teaching that empower students to design bugs in projects in mischievous and creative ways.

    

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4. Learning Generative Models of 3D Structures

   https://doi.org/10.1111/cgf.14020  

   Chaudhuri, Siddhartha ; Ritchie, Daniel ; Wu, Jiajun ; Xu, Kai ; Zhang, Hao ( July 2020 , Computer graphics forum)

   3D models of objects and scenes are critical to many academic disciplines and industrial applications. Of particular interest is the emerging opportunity for 3D graphics to serve artificial intelligence: computer vision systems can benefit from synthetically-generated training data rendered from virtual 3D scenes, and robots can be trained to navigate in and interact with real-world environments by first acquiring skills in simulated ones. One of the most promising ways to achieve this is by learning and applying generative models of 3D content: computer programs that can synthesize new 3D shapes and scenes. To allow users to edit and manipulate the synthesized 3D content to achieve their goals, the generative model should also be structure-aware: it should express 3D shapes and scenes using abstractions that allow manipulation of their high-level structure. This state-of-the- art report surveys historical work and recent progress on learning structure-aware generative models of 3D shapes and scenes. We present fundamental representations of 3D shape and scene geometry and structures, describe prominent methodologies including probabilistic models, deep generative models, program synthesis, and neural networks for structured data, and cover many recent methods for structure-aware synthesis of 3D shapes and indoor scenes. 

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5. Angular Gyrus Responses Show Joint Statistical Dependence with Brain Regions Selective for Different Categories

   https://doi.org/10.1523/JNEUROSCI.1283-22.2023  

   Fang, Mengting ; Aglinskas, Aidas ; Li, Yichen ; Anzellotti, Stefano ( April 2023 , The Journal of Neuroscience)

   Category selectivity is a fundamental principle of organization of perceptual brain regions. Human occipitotemporal cortex is subdivided into areas that respond preferentially to faces, bodies, artifacts, and scenes. However, observers need to combine information about objects from different categories to form a coherent understanding of the world. How is this multicategory information encoded in the brain? Studying the multivariate interactions between brain regions of male and female human subjects with fMRI and artificial neural networks, we found that the angular gyrus shows joint statistical dependence with multiple category-selective regions. Adjacent regions show effects for the combination of scenes and each other category, suggesting that scenes provide a context to combine information about the world. Additional analyses revealed a cortical map of areas that encode information across different subsets of categories, indicating that multicategory information is not encoded in a single centralized location, but in multiple distinct brain regions.

   SIGNIFICANCE STATEMENTMany cognitive tasks require combining information about entities from different categories. However, visual information about different categorical objects is processed by separate, specialized brain regions. How is the joint representation from multiple category-selective regions implemented in the brain? Using fMRI movie data and state-of-the-art multivariate statistical dependence based on artificial neural networks, we identified the angular gyrus encoding responses across face-, body-, artifact-, and scene-selective regions. Further, we showed a cortical map of areas that encode information across different subsets of categories. These findings suggest that multicategory information is not encoded in a single centralized location, but at multiple cortical sites which might contribute to distinct cognitive functions, offering insights to understand integration in a variety of domains. 

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