bibtext: @InProceedings{ Zeh_Rethinking_MICCAI2024,
                   author = { Zehra, Talat and Marino, Joseph and Wang, Wendy and Frantsuzov, Grigoriy and Nadeem, Saad },
                   title = { { Rethinking Histology Slide Digitization Workflows for Low-Resource Settings } },
                   booktitle = {Medical Image Computing and Computer Assisted Intervention -- MICCAI 2024},
                   year = {2024},
                   publisher = {Springer Nature Switzerland},
                   volume = { LNCS 15004 },
                   month = {October},
                   pages = { pending },
                }
abstract: Histology slide digitization is becoming essential for telepathology (remote consultation), knowledge sharing (education), and using the state-of-the-art artificial intelligence algorithms (augmented/automated end-to-end clinical workflows). However, the cumulative costs of digital multi-slide high-speed brightfield scanners, cloud/on-premises storage, and personnel (IT and technicians) make the current slide digitization workflows out-of-reach for limited-resource settings, further widening the health equity gap; even single-slide manual scanning commercial solutions are costly due to hardware requirements (high-resolution cameras, high-spec PC/workstation, and support for only high-end microscopes). In this work, we present a new cloud slide digitization workflow for creating scanner-quality whole-slide images (WSIs) from uploaded low-quality videos, acquired from cheap and inexpensive microscopes with built-in cameras. Specifically, we present a pipeline to create stitched WSIs while automatically deblurring out-of-focus regions, upsampling input 10X images to 40X resolution, and reducing brightness/contrast and light-source illumination variations. We demonstrate the WSI creation efficacy from our workflow on World Health Organization-declared neglected tropical disease, Cutaneous Leishmaniasis (prevalent only in the poorest regions of the world and only diagnosed by sub-specialist dermatopathologists, rare in poor countries), as well as other common pathologies on core biopsies of breast, liver, duodenum, stomach and lymph node. Upon acceptance, we will release our code, datasets, pretrained models, and cloud platform for uploading microscope videos and downloading/viewing WSIs with shareable links (no sign-in required) for telepathology and knowledge sharing.
title: Rethinking Histology Slide Digitization Workflows for Low-Resource Settings
authors: Zehra, Talat Marino, Joseph Wang, Wendy Frantsuzov, Grigoriy Nadeem, Saad