{"id":8330,"date":"2024-10-09T21:38:01","date_gmt":"2024-10-10T01:38:01","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?page_id=8330"},"modified":"2026-03-04T11:11:26","modified_gmt":"2026-03-04T16:11:26","slug":"digital-pathology-slides","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/resources\/data-ark\/digital-pathology-slides\/","title":{"rendered":"Digital Pathology Slides"},"content":{"rendered":"

[et_pb_section bb_built=”1″ fullwidth=”on” _builder_version=”4.9.0″ _module_preset=”default” next_background_color=”#000000″][et_pb_fullwidth_menu menu_id=”14″ menu_style=”centered” fullwidth_menu=”on” active_link_color=”#d80b8c” dropdown_menu_bg_color=”#221f72″ dropdown_menu_line_color=”#221f72″ dropdown_menu_active_link_color=”#d80b8c” _builder_version=”4.9.0″ _module_preset=”default” menu_font=”|600|||||||” menu_text_color=”#FFFFFF” menu_font_size=”16px” background_color=”#221f72″ background_layout=”dark” sticky_position=”top”]<\/p>\n

[\/et_pb_fullwidth_menu][\/et_pb_section][et_pb_section bb_built=”1″ _builder_version=”4.9.0″ _module_preset=”default” custom_padding=”0px||0px||false|false” prev_background_color=”#000000″ next_background_color=”#000000″][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_padding=”||0px||false|false”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Breadcrumb” _builder_version=”4.9.0″ _module_preset=”default”]<\/p>\n

Scientific Computing and Data<\/a> \/ Research Data Services<\/a> \/\u00a0Data Ark: Data Commons<\/a> \/ Digital Pathology Slides<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section bb_built=”1″ admin_label=”section” _builder_version=”4.9.0″ width=”100%” custom_padding=”0px||||false|false” prev_background_color=”#000000″][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|-12px|auto||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Header” _builder_version=”4.9.0″ _module_preset=”default” header_font=”|700|||||||” header_text_color=”#221f72″]<\/p>\n

De-identified Digital Pathology Slides<\/b><\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|35px|auto||” custom_padding=”28px|||||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Overview” _builder_version=”4.27.4″ _module_preset=”default” text_line_height=”1.5em” background_pattern_color=”rgba(0,0,0,0.2)” background_mask_color=”#ffffff” text_text_shadow_horizontal_length=”text_text_shadow_style,%91object Object%93″ text_text_shadow_horizontal_length_tablet=”0px” text_text_shadow_vertical_length=”text_text_shadow_style,%91object Object%93″ text_text_shadow_vertical_length_tablet=”0px” text_text_shadow_blur_strength=”text_text_shadow_style,%91object Object%93″ text_text_shadow_blur_strength_tablet=”1px” link_text_shadow_horizontal_length=”link_text_shadow_style,%91object Object%93″ link_text_shadow_horizontal_length_tablet=”0px” link_text_shadow_vertical_length=”link_text_shadow_style,%91object Object%93″ link_text_shadow_vertical_length_tablet=”0px” link_text_shadow_blur_strength=”link_text_shadow_style,%91object Object%93″ link_text_shadow_blur_strength_tablet=”1px” ul_text_shadow_horizontal_length=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_horizontal_length_tablet=”0px” ul_text_shadow_vertical_length=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_vertical_length_tablet=”0px” ul_text_shadow_blur_strength=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_blur_strength_tablet=”1px” ol_text_shadow_horizontal_length=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_horizontal_length_tablet=”0px” ol_text_shadow_vertical_length=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_vertical_length_tablet=”0px” ol_text_shadow_blur_strength=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_blur_strength_tablet=”1px” quote_text_shadow_horizontal_length=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_horizontal_length_tablet=”0px” quote_text_shadow_vertical_length=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_vertical_length_tablet=”0px” quote_text_shadow_blur_strength=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_blur_strength_tablet=”1px” header_text_shadow_horizontal_length=”header_text_shadow_style,%91object Object%93″ header_text_shadow_horizontal_length_tablet=”0px” header_text_shadow_vertical_length=”header_text_shadow_style,%91object Object%93″ header_text_shadow_vertical_length_tablet=”0px” header_text_shadow_blur_strength=”header_text_shadow_style,%91object Object%93″ header_text_shadow_blur_strength_tablet=”1px” header_2_text_shadow_horizontal_length=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_horizontal_length_tablet=”0px” header_2_text_shadow_vertical_length=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_vertical_length_tablet=”0px” header_2_text_shadow_blur_strength=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_blur_strength_tablet=”1px” header_3_text_shadow_horizontal_length=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_horizontal_length_tablet=”0px” header_3_text_shadow_vertical_length=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_vertical_length_tablet=”0px” header_3_text_shadow_blur_strength=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_blur_strength_tablet=”1px” header_4_text_shadow_horizontal_length=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_horizontal_length_tablet=”0px” header_4_text_shadow_vertical_length=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_vertical_length_tablet=”0px” header_4_text_shadow_blur_strength=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_blur_strength_tablet=”1px” header_5_text_shadow_horizontal_length=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_horizontal_length_tablet=”0px” header_5_text_shadow_vertical_length=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_vertical_length_tablet=”0px” header_5_text_shadow_blur_strength=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_blur_strength_tablet=”1px” header_6_text_shadow_horizontal_length=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_horizontal_length_tablet=”0px” header_6_text_shadow_vertical_length=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_vertical_length_tablet=”0px” header_6_text_shadow_blur_strength=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_blur_strength_tablet=”1px” box_shadow_horizontal_tablet=”0px” box_shadow_vertical_tablet=”0px” box_shadow_blur_tablet=”40px” box_shadow_spread_tablet=”0px” vertical_offset_tablet=”0″ horizontal_offset_tablet=”0″ z_index_tablet=”0″]<\/p>\n

Overview<\/h2>\n

\u00a0<\/p>\n

The Departments of Pathology, Molecular, & Cell Based Medicine, Windreich Department of AI and Human and Health, and Scientific Computing and Data, have collaborated to share this extensive digital archive of over 2.6 million whole slide images, collected from the Mount Sinai Anatomic Pathology and Consultation Service. These specimens encompass a broad spectrum of biopsies, resections, and autopsies, reflecting the diversity of diseases affecting patients from a wide range of backgrounds. Virtually every organ system is represented within this collection, including but not limited to the lung, heart, pancreas, kidney, liver, gastrointestinal, genitourinary, gynecological, hematological, and neuropathological systems. The disease processes span a wide array, encompassing neoplastic, developmental, inflammatory, toxic, metabolic, genetic, degenerative, traumatic, and infectious pathologies. The slides were prepared using a variety of staining techniques, from routine hematoxylin and eosin (H&E) to specialized stains like silver and trichrome, as well as immunohistochemistry. This rich dataset offers a unique and powerful resource for advancing the study of human disease through digital pathology.<\/span><\/p>\n

\u00a0<\/p>\n

\u00a0<\/p>\n

[\/et_pb_text][et_pb_text admin_label=”What Is Hosted Under Data Ark” _builder_version=”4.27.4″ _module_preset=”default” text_line_height=”1.5em” background_pattern_color=”rgba(0,0,0,0.2)” background_mask_color=”#ffffff” text_text_shadow_horizontal_length=”text_text_shadow_style,%91object Object%93″ text_text_shadow_horizontal_length_tablet=”0px” text_text_shadow_vertical_length=”text_text_shadow_style,%91object Object%93″ text_text_shadow_vertical_length_tablet=”0px” text_text_shadow_blur_strength=”text_text_shadow_style,%91object Object%93″ text_text_shadow_blur_strength_tablet=”1px” link_text_shadow_horizontal_length=”link_text_shadow_style,%91object Object%93″ link_text_shadow_horizontal_length_tablet=”0px” link_text_shadow_vertical_length=”link_text_shadow_style,%91object Object%93″ link_text_shadow_vertical_length_tablet=”0px” link_text_shadow_blur_strength=”link_text_shadow_style,%91object Object%93″ link_text_shadow_blur_strength_tablet=”1px” ul_text_shadow_horizontal_length=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_horizontal_length_tablet=”0px” ul_text_shadow_vertical_length=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_vertical_length_tablet=”0px” ul_text_shadow_blur_strength=”ul_text_shadow_style,%91object Object%93″ ul_text_shadow_blur_strength_tablet=”1px” ol_text_shadow_horizontal_length=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_horizontal_length_tablet=”0px” ol_text_shadow_vertical_length=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_vertical_length_tablet=”0px” ol_text_shadow_blur_strength=”ol_text_shadow_style,%91object Object%93″ ol_text_shadow_blur_strength_tablet=”1px” quote_text_shadow_horizontal_length=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_horizontal_length_tablet=”0px” quote_text_shadow_vertical_length=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_vertical_length_tablet=”0px” quote_text_shadow_blur_strength=”quote_text_shadow_style,%91object Object%93″ quote_text_shadow_blur_strength_tablet=”1px” header_text_shadow_horizontal_length=”header_text_shadow_style,%91object Object%93″ header_text_shadow_horizontal_length_tablet=”0px” header_text_shadow_vertical_length=”header_text_shadow_style,%91object Object%93″ header_text_shadow_vertical_length_tablet=”0px” header_text_shadow_blur_strength=”header_text_shadow_style,%91object Object%93″ header_text_shadow_blur_strength_tablet=”1px” header_2_text_shadow_horizontal_length=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_horizontal_length_tablet=”0px” header_2_text_shadow_vertical_length=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_vertical_length_tablet=”0px” header_2_text_shadow_blur_strength=”header_2_text_shadow_style,%91object Object%93″ header_2_text_shadow_blur_strength_tablet=”1px” header_3_text_shadow_horizontal_length=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_horizontal_length_tablet=”0px” header_3_text_shadow_vertical_length=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_vertical_length_tablet=”0px” header_3_text_shadow_blur_strength=”header_3_text_shadow_style,%91object Object%93″ header_3_text_shadow_blur_strength_tablet=”1px” header_4_text_shadow_horizontal_length=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_horizontal_length_tablet=”0px” header_4_text_shadow_vertical_length=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_vertical_length_tablet=”0px” header_4_text_shadow_blur_strength=”header_4_text_shadow_style,%91object Object%93″ header_4_text_shadow_blur_strength_tablet=”1px” header_5_text_shadow_horizontal_length=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_horizontal_length_tablet=”0px” header_5_text_shadow_vertical_length=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_vertical_length_tablet=”0px” header_5_text_shadow_blur_strength=”header_5_text_shadow_style,%91object Object%93″ header_5_text_shadow_blur_strength_tablet=”1px” header_6_text_shadow_horizontal_length=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_horizontal_length_tablet=”0px” header_6_text_shadow_vertical_length=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_vertical_length_tablet=”0px” header_6_text_shadow_blur_strength=”header_6_text_shadow_style,%91object Object%93″ header_6_text_shadow_blur_strength_tablet=”1px” box_shadow_horizontal_tablet=”0px” box_shadow_vertical_tablet=”0px” box_shadow_blur_tablet=”40px” box_shadow_spread_tablet=”0px” vertical_offset_tablet=”0″ horizontal_offset_tablet=”0″ z_index_tablet=”0″]<\/p>\n

What Is Hosted Under Data Ark?<\/h2>\n

\u00a0<\/p>\n

Currently, Data Ark hosts 2.6 million de-identified digital pathology slides and more slides will be made available on a continuing basis. Digital pathology slides have been linked to patients\u2019 EHR (electronic health record), and EHR data is available from Mount Sinai Data Warehouse. Slides were scanned on the Philips Ultrafast or other system at 40x magnification. iSyntax files were converted to TIF. Slides served through Data Ark have been de-identified and digitized into a readable TIF format\u200b.<\/p>\n

[\/et_pb_text][et_pb_image admin_label=”Pathology Slide” src=”https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/10\/DigitalPathologySlides.png” title_text=”DigitalPathologySlides” align=”center” _builder_version=”4.27.4″ _module_preset=”default” width=”80%” max_width=”80%” custom_margin=”10px||||false|false”]<\/p>\n

[\/et_pb_image][et_pb_text admin_label=”Pathology Slide Caption” _builder_version=”4.9.0″ _module_preset=”default” text_line_height=”1.5em” width=”80%” max_width=”80%” module_alignment=”center” custom_margin=”50px||||false|false”]<\/p>\n

Figure 1. Digitized pathology slides are gigapixel images that can span hundreds of thousands of pixels in each dimension.<\/p>\n

[\/et_pb_text][et_pb_text admin_label=”Demographics” _builder_version=”4.27.4″ _module_preset=”default” custom_margin=”50px||||false|false”]<\/p>\n

Digital pathology slides were collected from 191,119<\/span> patients through October 1, 2024, with demographic information detailed below.<\/p>\n

[\/et_pb_text][et_pb_text admin_label=”Table Caption” _builder_version=”4.9.0″ _module_preset=”default” text_line_height=”1.5em” custom_margin=”30px||||false|false”]<\/p>\n

Table 1. Cohort demographics: (a) gender, (b) race and ethnicity, and (c) age.<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row admin_label=”Tables” column_structure=”1_3,1_3,1_3″ _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”0px||0px||false|false”][et_pb_column type=”1_3″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_code admin_label=”Gender Table” _builder_version=”4.9.0″ _module_preset=”default” width=”40%” max_width=”40%” module_alignment=”left” custom_margin=”-100px||||false|false”](a)<\/p>\n<\/p>\n\n\n <\/p>\n\n\n\n\n
Gender<\/th>\nCount<\/th>\n<\/tr>\n<\/thead>\n
Female<\/td>\n120,121<\/td>\n<\/tr>\n

<\/p>\n

Indeterminate<\/td>\n13<\/td>\n<\/tr>\n

<\/p>\n

Male<\/td>\n70,945<\/td>\n<\/tr>\n

<\/p>\n

Unknown<\/td>\n40<\/td>\n<\/tr>\n

<\/tbody>\n<\/table>\n

[\/et_pb_code][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_code admin_label=”Race Ethnicity Table” _builder_version=”4.9.0″ _module_preset=”default” width=”97%” max_width=”97%” module_alignment=”center” custom_margin=”-100px||||false|false”](b)<\/p>\n<\/p>\n\n\n <\/p>\n\n\n\n\n\n\n\n\n
Race Ethnicity Combined<\/th>\nCount<\/th>\n<\/tr>\n<\/thead>\n
American Indian or Alaska Native<\/td>\n140<\/td>\n<\/tr>\n

<\/p>\n

Asian<\/td>\n14,071<\/td>\n<\/tr>\n

<\/p>\n

Black or African-American<\/td>\n28,323<\/td>\n<\/tr>\n

<\/p>\n

Hispanic<\/td>\n35,508<\/td>\n<\/tr>\n

<\/p>\n

Native Hawaiian or Pacific Islander<\/td>\n159<\/td>\n<\/tr>\n

<\/p>\n

Patient Declined<\/td>\n958<\/td>\n<\/tr>\n

<\/p>\n

White<\/td>\n66,515<\/td>\n<\/tr>\n

<\/p>\n

Unknown\/Other\/Not Reported<\/td>\n45,445<\/td>\n<\/tr>\n

<\/tbody>\n<\/table>\n

[\/et_pb_code][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_code admin_label=”Age Group” _builder_version=”4.9.0″ _module_preset=”default” width=”62%” max_width=”62%” module_alignment=”right” custom_margin=”-100px||||false|false”](c)<\/p>\n<\/p>\n\n\n <\/p>\n\n\n\n\n\n\n\n\n\n\n
Age Group<\/th>\nCount<\/th>\n<\/tr>\n<\/thead>\n
0-10<\/td>\n1,377<\/td>\n<\/tr>\n

<\/p>\n

11-20<\/td>\n3,239<\/td>\n<\/tr>\n

<\/p>\n

21-30<\/td>\n14,950<\/td>\n<\/tr>\n

<\/p>\n

31-40<\/td>\n28,684<\/td>\n<\/tr>\n

<\/p>\n

41-50<\/td>\n31,704<\/td>\n<\/tr>\n

<\/p>\n

51-60<\/td>\n35,551<\/td>\n<\/tr>\n

<\/p>\n

61-70<\/td>\n38,128<\/td>\n<\/tr>\n

<\/p>\n

71-80<\/td>\n26,597<\/td>\n<\/tr>\n

<\/p>\n

81-90<\/td>\n9,424<\/td>\n<\/tr>\n

<\/p>\n

91+<\/td>\n1,465<\/td>\n<\/tr>\n

<\/tbody>\n<\/table>\n

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Access<\/h2>\n

\u00a0<\/p>\n

To use this data, you must read, agree and sign the Data Use Agreement<\/a> (you must be logged in through the Mount Sinai campus network or secure remote VPN). IRB (Institutional Review Board) approval is not required to access Digital Pathology Slide data via Data Ark.<\/span><\/p>\n

After granted access, you can access the slides by going to the folder on Minerva directly. To get the path variable, you can load the module by issuing the command $ module load dataark<\/strong>.<\/span><\/p>\n

In addition, we are also working on the Digital Slide Archive web application for interactive slide viewer and annotation (coming soon).<\/p>\n

Further details about how to use these slides in your research can be found here: \u00a0\u00a0<\/p>\n