Human pancreas 3D — from organ to cell

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An explorable 3D model of the human pancreas that you can zoom through continuously: from the whole organ (about 15 cm) opened in place layer by layer through its lobules and duct tree to a core of tissue, then a single acinus, islet or duct, its separated cells, and finally one cell with its organelles — all at true scale, in H&E or cell-type colours, with an optional narrated tour.

The idea

Why I built this

This project grew out of personal curiosity: I wanted to understand the pancreas better. It is a single organ that holds two very different units: an exocrine part that makes digestive enzymes, and an endocrine part, the islets, that controls blood sugar. When either one goes wrong, the result can be a debilitating disease: diabetes from the endocrine side, and pancreatitis and pancreatic ductal adenocarcinoma from the exocrine side.

As a bioinformatician, I am always curious about the biology behind the diseases I study in data. This project gathers some of what I have learned while working on pancreatic cancer research, and I built it to see that biology in three dimensions and to share it with others.

Seeing the scales together

The pancreas is usually taught in pieces: a gross-anatomy drawing in one lecture, an H&E slide in another, a cartoon of an acinar cell in a third. It is hard to hold in one's head how those scales connect — where an islet sits relative to the main duct, how many acini drain into one intercalated duct, what a beta cell looks like next to its capillary.

This project puts those scales into one continuous space so a learner can move between them. It is built as a learning tool for students, trainees and researchers, and as a scaffold for showing where disease begins (see Next steps).

It is also built to be honest about what it knows. Every structure carries one of three labels, and the viewer shows it:

• source — drawn by the Human Reference Atlas from the Visible Human Project (organ shape, main ducts, large vessels);
• traced — followed from a published image;
• simulated — placed by a written rule from published measurements (small vessels, lymph nodes, lobules, acini, islets, cells).

Every number either names its source or is marked not yet sourced in the code, and the tests fail if one is missing.

What you can see

The organ, opened layer by layer

The reference pancreas (head, neck, body, tail, uncinate process) with the main and accessory pancreatic ducts, bile duct and ampulla, and the coeliac, splenic, hepatic and superior mesenteric vessels. Thirty tissue sites (ten each in head, body and tail, scattered at random) lie hidden in the gland, each showing its region's tissue (islets in the uncinate process are rich in PP cells): zoom in on any part of the organ and one of the sites nearest the pointer is picked at random and brought to the middle of the view.

Zooming into a site opens the gland in place, layer by layer, the way MouseBio_3D opens the mouse: a line goes into the gland at the site, and as you zoom the organ's surface opens round it. Inside, the lobules stand cut across, with pale septa of connective tissue between them. Round the line, the lobules near the site open in turn to show what fills them: the duct tree (large interlobular duct with its artery and vein, interlobular, intralobular and terminal ducts ending in grape-like clusters of acini) and the islets, twice as dense in the tail as in the head. At the bottom of the opening lies a core of tissue, cut flat through its islet. Each outer layer stays as a ring round the next, and zooming out closes them again.

Organ	The surface opens	Lobules and their ducts	Tissue core

Compare head, body and tail puts the three regions' lobule columns side by side, each opened to its duct tree and islets:

Inside the tissue: how the pancreas works

The pancreas is two organs in one, and the model shows both:

• Exocrine (digestion) — about 98% of the tissue. Wedge-shaped acinar cells arranged like orange segments around a tiny lumen make digestive enzymes: rough ER around the basal nucleus synthesises them, the Golgi packages them, and zymogen granules wait at the cell apex for release. Each acinus empties into its own intercalated duct, lined at its start by centroacinar cells; ducts merge into intralobular, interlobular and finally the main pancreatic duct, which joins the bile duct at the ampulla in the duodenum. Duct cells add bicarbonate-rich fluid (through CFTR and SLC26A6) that carries the enzymes and neutralises stomach acid.
• Endocrine (blood sugar) — about 1–2%. Islets of Langerhans (about 110 µm, a few hundred cells each) contain beta cells (insulin), alpha cells (glucagon), delta cells (somatostatin) and PP cells, intermixed along a dense capillary bed as in human islets. A beta cell is shown with its insulin granules (dense crystalline cores in pale halos), primary cilium and neighbouring capillary.

Acinus	Islet (cell-type colours)	Acinar cell	Beta cell

This is the beginning of the README. Read the rest at the original. Read the full README ↗