Abstract Pancreatlas (https://pancreatlas.org/) is an online resource that houses and links human pancreas imaging data with clinical data to facilitate advances in the understanding of diabetes, pancreatitis, and pancreatic cancer. Increasingly, human tissue phenotyping programs and projects are generating complex data from numerous imaging modalities, yet only a fraction are shared as static figures for publication. We built Pancreatlas to bring together imaging data under a standardized, intuitive, and interactive platform that is publicly accessible and connects data from disparate research efforts in order to accelerate discovery science. Pancreatlas currently contains over 1,800 full-resolution images organized across seven context-aware collections, including whole-slide images of histological stains and fluorescent immunohistochemical labeling, multiplex modalities CODEX and imaging mass cytometry, and confocal microscopy. Pancreatlas utilizes an open-source web application and application programming interface (API) framework (Flexible Framework for Integrating and Navigating Data; FFIND; https://github.com/Powers-Brissova-Research-Group/FFIND) and a back-end instance of Open Microscopy Environment Remote Objects Plus (OMERO Plus, Glencoe Software), which together integrate domain-specific data exploration with interactive image viewing (PathViewer, Glencoe Software). Looking ahead, we plan to expand connectivity and integration with other platforms and pancreas mapping efforts, including development of a graph database, improved annotations and ontologies, and enhanced search and browsing, as well as expanding connections between imaging and other omics resources. The top 4 key questions that Pancreatlas can answer: 1. How does the architecture of the human pancreas change during the first decade of life? 2. What compositional alterations occur in islets from donors with type 1 and type 2 diabetes? 3. Which markers can be used to visualize non-endocrine cell types in human pancreas? 4. How much variation exists across histological features of clinically “normal” pancreata? Presenters: Marcela Brissova, PhD, Research Professor, Vanderbilt University Medical Center Jean-Philippe Cartailler, PhD, Director of Creative Data Solutions, Vanderbilt University Diane Saunders, PhD, Research Instructor, Vanderbilt University Medical Center Upcoming webinars schedule: https://dknet.org/about/webinar

1. Pancreatlas™:
Mapping the Human Pancreas in
Health and Disease
dkNET Webinar • January 28, 2022

2. dkNET webinar 01.28.2022 (2 of 30)
Presentation outline
Rationale for
creation
Technical
background,
applicability,
& integration
Site tour
& use case
examples
Future
plans and
community
input
Diane Saunders
Imaging scientist & artist
JP Cartailler
Bioinformatician &
database designer
Diane Saunders Marcela Brissova
Islet biologist & phenotyping
program director

3. dkNET webinar 01.28.2022 (3 of 30)
Breadth of human pancreatic research
Pancreas
• Diabetes
• Chronic pancreatitis
• Pancreatic cancer
• Cystic fibrosis
Image © 2014 Pearson Education, Inc.
Head Body Tail
Main pancreatic
duct
Blood vessel
Acinar cells
Pancreatic islet
(endocrine cells)
Common
bile duct
Duodenum
Accessory
pancreatic duct
Major duodenal
papilla
Pancreatic
ducts
Pancreatic acini

4. dkNET webinar 01.28.2022 (4 of 30)
Network for Pancreatic Organ
Donors with Diabetes
https://www.jdrfnpod.org
Human Pancreas Analysis Program
https://hpap.pmacs.upenn.edu/
Human Atlas of the Neonatal
and Early Life Pancreas
HANDEL-P data
Human Islet Phenotyping Program of IIDP
IIDP-HIPP data
The Human BioMolecular Atlas Program
https://hubmapconsortium.org
Resources generating data from human pancreas

5. dkNET webinar 01.28.2022 (5 of 30)
Pancreas tissue procurement in the U.S.
• Cases identified 24/7/365 via Organ
Procurement Organizations (OPOs)
• 57 OPOs in the United States; nPOD
works with 100%:
ü 10 OPOs directly
ü 47 OPOs indirectly through research
intermediaries: IIAM, NDRI, and
Promethera
Donation Service
Areas (2016)

6. dkNET webinar 01.28.2022 (6 of 30)
Building an atlas for human pancreas images
Capture &
integrate
donor
information
Z-stacks and
3D projections
Traditional
immunofluorescence
Whole-slide scans
Multiplexed
immunohistochemistry
Display
images in
meaningful,
intuitive
platform

7. dkNET webinar 01.28.2022 (7 of 30)
Pancreatlas as a connectivity platform

8. dkNET webinar 01.28.2022 (8 of 30)
Prioritizing usability and accessibility
Challenges of large datasets Ideal platform capabilities
• Image quantity and size User-friendly interface
• Varied file types Out-of-box support for common and
proprietary image types
• Associated metadata Annotation with pertinent information
(donor attributes, etc.)
• Static publication
Support for 4+ independent channels and
ability to interact with them

9. dkNET webinar 01.28.2022 (9 of 30)
Presentation outline
Rationale for
creation
Technical
background,
applicability,
& integration
Site tour
& use case
examples
Future
plans and
community
input
JP Cartailler

10. dkNET webinar 01.28.2022 (10 of 30)
In addition to prioritizing usability and accessibility…
• Do not re-invent the wheel
• User-friendly and online tools (nothing to download or install)
• Support all image formats
• Scalable and flexible (as much as funding can support)
Usability
and friendly to
biologists
Complexity
and flexibility for
developers
Achieving a technical balance

11. dkNET webinar 01.28.2022 (11 of 30)
IT
infrastructure
Custom web
interface
LIMS
Private network Public (internet)
Users can access an interactive, full-featured
image viewer through easy-to-navigate
web pages that serve as curated points of entry
to large datasets
Pancreatlas integrates donor information with
multi-modality images
Image
storage
Software platform for
image management
and analysis

12. dkNET webinar 01.28.2022 (12 of 30)
.mrxs .sld .tif .aim .al3d .gel .am .grey .hx .labels .cif .img .hdr .sif .png .afi .svs .htd .pnl .avi
.arf .exp, .tif .spc .sdt .1sc .pic .raw .xml .scn .ims .img .cr2 .crw .ch5 .c01 .dib .vsi .xml .tif
.wpi .tif .dv .r3d .dcm .dicom .v .eps .epsi .ps .flex .mea .res .img .tiff .fits .dm3 .dm4 .dm2
.gif .naf .his .ndpi .ndpis .vms .txt .tif .bmp .jpg .i2i .ics .ids .fff .seq .ipw .hed .img .mod .liff
.raw .tif .obf .msr .xdce .tif .frm .inr .hdr .ipl .ipm .dat .img .par .jpg .jp2 .jpk .jpx .xv .bip .fli
.msr .lei .tif .lif .scn .sxm .l2d .tif .scn .lim .tiff .stk .nd .tif .tif .txt .xml .mnc .mrw .mng .stp
.mrc .nef .img .hdr .nii .nii.gz .nd2 .nrrd .nhdr .raw .apl .mtb .tnb .obsep .oib .oif .oir .xml
.ome.tiff .ome.tif .ome.tf2 .ome.tf8 .ome.btf .ome .ome.xml .top .pcoraw .rec .pcx .pds .xml
.csv .im3 .pbm .pgm .ppm .psd .bin .pict .png .cfg .spe .afm .mov .sm2 .sm3 .xqd .xqf .cxd
.spi .stk .tga .tf2 .tf8 .btf .vws .tfr .ffr .zfr .zfp .2fl .sld .pr3 .dat .hdr .fdf .hdf .dti .xys .html
.mvd2 .acff .wat .bmp .wlz .lms .zvi .czi .lsm .mdb
Organizing, sharing, and viewing image data
150+
file formats
OME
-Zarr
Leveraging Glencoe software capabilities

13. dkNET webinar 01.28.2022 (13 of 30)
React for UI
A JavaScript library for
building user interfaces
Django for API
A high-level Python web
framework
OMERO
PathViewer
Web app and API development
• 100% focus on end-user
• Rapid development & re-usable components
• Common web interface idioms
• Large community for support and ideas
• Machine-friendly!
• Metadata retrieval from OMERO
• Stubs in place for non-OMERO data
• Future public-facing API
Biologists
Analysts

14. dkNET webinar 01.28.2022 (14 of 30)
• FFIND is a data-agnostic version of
Pancreatlas
• It can be used for any kind of data,
not just imaging
Open-source FFIND
Flexible Framework for Integrating and Navigating Data
• It takes just two minutes to get the
front-end app up-and-running!
• Mock flat-file datasets provided to
play with
https://github.com/Powers-Brissova-Research-Group/FFIND

15. dkNET webinar 01.28.2022 (15 of 30)
Spreadsheet-based metadata import
Filters
Pancreas Region
Imaging Modality
Disease Status
Sex
Age
Each row of metadata corresponds to one image
Columns= researcher-defined variables
Import script

16. dkNET webinar 01.28.2022 (16 of 30)
Current collections feature over
full-resolution images
Alan Foulis Collection
Exeter Archival Diabetes Biobank
Coming soon!
M
Manuscript Phenotyping program
M P
M
P M P M P
M
P P
1,800

17. dkNET webinar 01.28.2022 (17 of 30)
Growth of Pancreatlas over time
367
709
844
950
1,723
1,835

18. dkNET webinar 01.28.2022 (18 of 30)
Usage, as measured by Google Analytics
Manuscript on bioRxiv
Manuscript in Patterns
1.0 1.1 1.2 1.3 1.4 1.5
June 1, 2019 – January 27, 2021

19. dkNET webinar 01.28.2022 (19 of 30)
Presentation outline
Rationale for
creation
Technical
background,
applicability,
& integration
Site tour
& use case
examples
Future
plans and
community
input
Diane Saunders

20. dkNET webinar 01.28.2022 (20 of 30)
Key research questions that data from
Pancreatlas can help answer
1. How does the architecture of the human pancreas change during the
first decade of life?
2. What cell- and tissue-level alterations occur in individuals with type 1
and type 2 diabetes?
3. How much variation exists across histological features of clinically
“normal” pancreata?
4. Which markers can be used to visualize exocrine, ductal, stromal,
immune, and other cell types in the human pancreas?

21. dkNET webinar 01.28.2022 (21 of 30)
Demo/site tour
www.pancreatlas.org

22. dkNET webinar 01.28.2022 (22 of 30)
Presentation outline
Rationale for
creation
Technical
background,
applicability,
& integration
Site tour
& use case
examples
Future
plans and
community
input
Marcela Brissova

23. dkNET webinar 01.28.2022 (23 of 30)
Looking ahead…
• Knowledge graph
• Improved compliance with FAIR
principles
• Addition of ontologies
• Enhanced search and browsing
capabilities
• Connection of imaging data with
other omics datasets
• Cloud migration and analysis
opportunities
Technical advances Feature-based development
https://hubmapconsortium.github.io/ccf/
Katy Börner, Ellen Quardokus

24. dkNET webinar 01.28.2022 (24 of 30)
Looking ahead…
Enhance search and browsing features
• View all datasets together in one
grid
• Search and filter across
images/collections to identify
data of interest
• Improved layout of donor and
sample filters

25. dkNET webinar 01.28.2022 (25 of 30)
Looking ahead…
Connecting imaging and omics resources
Data exploration,
integration, and
analysis
Genetic risk and variants
Transcriptomic and
epigenomic profiling
Tissue imaging and
architecture
Clinical history &
demographics
Physiology and function

26. dkNET webinar 01.28.2022 (26 of 30)
Looking ahead…
Connecting imaging and omics resources
Imaging data Omics data
Specialized viewer
Specialized viewer

27. dkNET webinar 01.28.2022 (27 of 30)
Looking ahead…
Cloud migration & opportunities
Increased
scalability
Ease of data upload for
external collaborators
Ability to conduct
image analysis
directly in cloud
Easier to access raw
imaging data

28. dkNET webinar 01.28.2022 (28 of 30)
Consortium for the Study of
Chronic Pancreatitis, Diabetes,
and Pancreatic Cancer (CPDPC)
Potential future connection
Pancreatlas as a connectivity platform
Established connection

29. We are especially grateful to organ donors and their families.
dkNET webinar 01.28.2022 (29 of 30)
Acknowledgements
Marcela Brissova
JP Cartailler
Samuel Johnson
Marcelo Pineda
Al Powers
Diane Saunders
Jimmy Messmer
Data curation:
Alexander Hopkirk
Conrad Reihsmann
UF/nPOD: Irina Kusmartseva, Mingder Yang
HANDEL: Maigan Brusko, Todd Brusko
HuBMAP: Martha Campbell-Thompson,
Clayton Matthews, Jeff Spraggins
Mark Atkinson
Rita Bottino
Nathaniel Hart
Klaus Kaestner
Seung Kim
Noel Morgan
Fong Chen Pan
Sarah Richardson
Jack Walker
Christopher Wright
Jordan Wright
Pancreatlas Team Collaborators
Contributors

30. dkNET webinar 01.28.2022 (30 of 30)
We would love to connect!
Feedback or suggestions? pancreatlas@vumc.org
Imaging datasets to publish? Please contact Diane (diane.saunders@vumc.org)
Interested in joining our team? We are hiring for positions of Graph Database
Developer, Data Curator/Biostatistician, and Project Manager
@pancreatlas
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