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1. 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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2. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

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3. PoseASL: An RGBD Dataset of American Sign Language

   https://doi.org/10.17910/b7.1279  

   Huenerfauth, Matt ( January 2021 , Databrary)

   The PoseASL dataset consists of color and depth videos collected from ASL signers at the Linguistic and Assistive Technologies Laboratory under the direction of Matt Huenerfauth, as part of a collaborative research project with researchers at the Rochester Institute of Technology, Boston University, and the University of Pennsylvania. Access: After becoming an authorized user of Databrary, please contact Matt Huenerfauth if you have difficulty accessing this volume. We have collected a new dataset consisting of color and depth videos of fluent American Sign Language signers performing sequences ASL signs and sentences. Given interest among sign-recognition and other computer-vision researchers in red-green-blue-depth (RBGD) video, we release this dataset for use by the research community. In addition to the video files, we share depth data files from a Kinect v2 sensor, as well as additional motion-tracking files produced through post-processing of this data. Organization of the Dataset: The dataset is organized into sub-folders, with codenames such as "P01" or "P16" etc. These codenames refer to specific human signers who were recorded in this dataset. Please note that there was no participant P11 nor P14; those numbers were accidentally skipped during the process of making appointments to collect video stimuli. Task: During the recording session, the participant was met by a member of our research team who was a native ASL signer. No other individuals were present during the data collection session. After signing the informed consent and video release document, participants responded to a demographic questionnaire. Next, the data-collection session consisted of English word stimuli and cartoon videos. The recording session began with showing participants stimuli consisting of slides that displayed English word and photos of items, and participants were asked to produce the sign for each (PDF included in materials subfolder). Next, participants viewed three videos of short animated cartoons, which they were asked to recount in ASL: - Canary Row, Warner Brothers Merrie Melodies 1950 (the 7-minute video divided into seven parts) - Mr. Koumal Flies Like a Bird, Studio Animovaneho Filmu 1969 - Mr. Koumal Battles his Conscience, Studio Animovaneho Filmu 1971 The word list and cartoons were selected as they are identical to the stimuli used in the collection of the Nicaraguan Sign Language video corpora - see: Senghas, A. (1995). Children’s Contribution to the Birth of Nicaraguan Sign Language. Doctoral dissertation, Department of Brain and Cognitive Sciences, MIT. Demographics: All 14 of our participants were fluent ASL signers. As screening, we asked our participants: Did you use ASL at home growing up, or did you attend a school as a very young child where you used ASL? All the participants responded affirmatively to this question. A total of 14 DHH participants were recruited on the Rochester Institute of Technology campus. Participants included 7 men and 7 women, aged 21 to 35 (median = 23.5). All of our participants reported that they began using ASL when they were 5 years old or younger, with 8 reporting ASL use since birth, and 3 others reporting ASL use since age 18 months. Filetypes: *.avi, *_dep.bin: The PoseASL dataset has been captured by using a Kinect 2.0 RGBD camera. The output of this camera system includes multiple channels which include RGB, depth, skeleton joints (25 joints for every video frame), and HD face (1,347 points). The video resolution produced in 1920 x 1080 pixels for the RGB channel and 512 x 424 pixels for the depth channels respectively. Due to limitations in the acceptable filetypes for sharing on Databrary, it was not permitted to share binary *_dep.bin files directly produced by the Kinect v2 camera system on the Databrary platform. If your research requires the original binary *_dep.bin files, then please contact Matt Huenerfauth. *_face.txt, *_HDface.txt, *_skl.txt: To make it easier for future researchers to make use of this dataset, we have also performed some post-processing of the Kinect data. To extract the skeleton coordinates of the RGB videos, we used the Openpose system, which is capable of detecting body, hand, facial, and foot keypoints of multiple people on single images in real time. The output of Openpose includes estimation of 70 keypoints for the face including eyes, eyebrows, nose, mouth and face contour. The software also estimates 21 keypoints for each of the hands (Simon et al, 2017), including 3 keypoints for each finger, as shown in Figure 2. Additionally, there are 25 keypoints estimated for the body pose (and feet) (Cao et al, 2017; Wei et al, 2016). Reporting Bugs or Errors: Please contact Matt Huenerfauth to report any bugs or errors that you identify in the corpus. We appreciate your help in improving the quality of the corpus over time by identifying any errors. Acknowledgement: This material is based upon work supported by the National Science Foundation under award 1749376: "Collaborative Research: Multimethod Investigation of Articulatory and Perceptual Constraints on Natural Language Evolution." 

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4. Shining a New Light on Elmer Ottis Wooton’s Legacy Herbarium and Historical Archive: an Exercise to Increase Student Participation while Promoting Public Engagement

   https://doi.org/10.3897/biss.2.25783  

   Fuentes-Soriano, Sara ; Prihodko, Lara ; Manford, Mitchell ; Rogers, Zachary ( June 2018 , Biodiversity Information Science and Standards)

   Elmer Ottis Wooton (1865–1945) was one of the most important early botanists to work in the Southwestern United States, contributing a great deal of natural history knowledge and botanical research on the flora of New Mexico that shaped many naturalists and scientists for generations. The extensive Wooton legacy includes herbarium collections that he and his famous student Paul Carpenter Standley (1884–1963), prolific botanist and explorer, used for the first Flora of New Mexi co by Wooten and Standley 1915 , along with resources covering botany and range management strategies for the northern Chihuahuan Desert, and an extensive, yet to be digitized, historical archive of correspondence, field notes, vegetation sketches, photographs, and lantern slides, all from his travels and field work in the region. Starting in 1890, the most complete set of Wooton’s herbarium collections were deposited in the NMC herbarium at New Mexico State University (NMSU), and his archives, now stored in a Campus library, have together been underutilized, offline resources. The goals of this ongoing project are to secure, preserve, and promote Wooton’s important historical resources, by fleshing out the botanical history of the region, raising appreciation of herbarium collections within the community, and emphasizing their unique role in facilitating contemporary research aimed at addressing pressing scientific questions such as vegetation responses to global climate change. Students and the general public involved in this project are engaged through hands-on activities including cataloging, databasing and digitization of nearly 10,000 herbarium specimens and Wooton’s archives. These outputs, combined with contemporary data collection and computational biology techniques from an ecological perspective, are being used to document vegetation changes in iconic, climate-sensitive, high-elevation mountainous ecosystems present in southwestern New Mexico. In a later phase of the project, a variety of public audiences will participate through interactive online story maps and citizen science programs such as iNaturalist , Notes from Nature , and BioBlitz . Images of herbarium specimens will be shared via an online database and other relevant biodiversity portals ( Symbiota , iDigBio , JStor ) Community members reached through this project will be better-informed citizens, who may go on to become new stewards of natural history collections, with the potential to influence policies safeguarding the future of our planet’s biodiversity. More locally, the project will support the management of Organ Mountains Desert Peaks National Monument, which was established in 2014 to protect the area's human and environmental resources, and for which knowledge and data are currently limited. 

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5. PiAutoStage: An Open‐Source 3D Printed Tool for the Automatic Collection of High‐Resolution Microscope Imagery

   https://doi.org/10.1029/2021GC009693  

   Steiner, R. Alex ; Rooney, Tyrone O. ( May 2021 , Geochemistry, Geophysics, Geosystems)

   We have created an open‐source 3D printable microscope automatic stage and integrated camera system capable of providing a means for imaging microscope slides—the PiAutoStage. The PiAutoStage was developed to interface with the high‐quality optics of existing microscopes by creating an adaptable system that can be used in conjunction with a range of microscope configurations. The PiAutoStage automatically captures the entire area of a microscope slide in a series of overlapping high‐resolution images, which can then be stitched into a single panoramic image. We have demonstrated the utility of the PiAutoStage when attached to a transmitted light microscope by creating high‐fidelity image stacks of rock specimens in plane polarized and cross‐polarized light. We have shown that the PiAutoStage is compatible with microscopes that do not currently have a camera attachment by using two different optical trains within the same microscope: one set of imagery collected through the photography tube of a trinocular microscope, and a second set through a camera mounted to an ocular. We furthermore establish the broad adaptability of the PiAutoStage system by attaching it to a reflected light stereo dissection microscope to capture images of microfossils. We discuss strategies for the online delivery of these large‐sized images in a data efficient manner through the application of tiled imagery and open‐source Java‐based web viewers. The low cost of the PiAutoStage system, combined with the data‐efficient mechanisms of online delivery make this system an important tool in promoting the universal accessibility of high‐resolution microscope imagery.

    

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