Embryo

Embryo draws one published recording: the nuclei files of the WormGUIDES atlas (Santella et al. 2015, BMC Bioinformatics 16:189), read from its public repository at commit 17be611. It is one individual Caenorhabditis elegans embryo — strain JIM113, image series DISPIM_061416, imaged uncompressed on a light-sheet microscope, one frame a minute — whose nuclei were tracked automatically and then curated by the atlas’s authors.

Cell names follow Sulston et al. (1983, Developmental Biology 100:64–119). Fates come from two files in the same repository, the parts list and the list of programmed cell deaths, both after Sulston. The faint outline is the atlas’s own “Embryo Outline” mesh.

The source repository is licensed GPL-3.0 and declares no separate data licence. The files Embryo loads are derived from it, so they are published under GPL-3.0 as well, with a notice beside them naming the source, the commit and what was changed.

The published files are content-addressed: build a829bdbfd6c7, published 2026-09-18, 1.6 MB in all. A new export is a new build with a new address, so a shared link never silently changes what it shows.

360 recorded minutes, from 4 cells to 580. Over the whole recording 1,330 cells are tracked, at 106,275 measured positions — one per cell per minute it exists, with no gaps.

663 cells are seen dividing, each into exactly two observed daughters born the minute after the mother’s last. 113 tracked cells are on the published list of programmed cell deaths.

Of the 580 cells alive at the last minute, the published parts list names a fate for 553. The rest are shown without one.

Each ball is one cell nucleus — not the whole cell — at the position and the diameter the atlas records for that minute. Nothing is interpolated, smoothed or imputed in the published files: the horizontal position and the diameter are stored exactly, the depth to within 1/512 of a voxel.

Units are the microscope’s voxels. The source declares no physical size, so Embryo shows no scale bar and states no length.

The view is turned so that up is up and the embryo’s left stays its left; nothing is mirrored. The head-end and tail-end labels follow the axis the source declares.

The recording is one frame a minute. Between two frames Embryo draws a straight line from one measured position to the next — for a division, from the mother’s last position to each daughter’s first. That in-between motion is drawn, not measured, and the readout under the timeline says so while it happens. The view settings can turn it off, and the embryo then steps from minute to minute.

A cell whose track ends shrinks out over its last minute; every such cell is on the published list of programmed deaths.

The outline is switched, one mesh per recorded minute, never blended. The repository does not document how it was traced, so Embryo calls it a modelled outline, not an eggshell. It holds still until minute 252 and then begins to bend.

A cell’s name is its ancestry: every letter is one division — a and p for the front and back daughter, l and r for left and right, d and v for top and bottom. That is how Embryo finds a cell’s ancestors, its descendants and its relatives: by reading names, never by guessing from positions.

Colour is the founder family: the 6 founding cells AB, MS, E, C, D and P4, plus a grey for the few early cells that exist before the founders have split off. What each family goes on to become, as the legend words it, is after Sulston et al. 1983 — general knowledge about the species, not something this recording shows.

A fate is the published parts list’s own wording, copied as is and only for a cell the list names. It is never inferred, and never passed from a cell to its relatives. For a cell that divides, the caption counts the published fates of its final descendants.

Several family colours are hard to tell apart under some kinds of colour blindness, which is why the legend and the caption always name the family in words as well.

Cite Embryo with its build and publication date; together they pin exactly the files you saw:

Grove Lab. Embryo, build a829bdbfd6c7, published 2026-09-18. https://grove-lab.org/en/embryo (accessed 2026-09-19).

Embryo re-draws a published recording, so a claim about a cell, a position or a fate should cite where it comes from: Santella et al. 2015 for the recording and the atlas, and Sulston et al. 1983 for the lineage and the fates. Both are listed under Source and licence.

For a specific view, link the view itself: explore links (/embryo/explore?…) carry the minute, the kept cell and the camera, so the link you share opens where you were.

Embryo is only as complete as the recording it draws. Its limits are the recording’s limits, plus the choices named above:

• It is one embryo. Nothing here is an average, and nothing says how much another embryo would differ.
• It ends at minute 360, with 580 cells and a first bend — not a worm. Soon after, the embryo starts to move inside its shell, which is what stops this kind of tracking.
• It starts at 4 cells. The first divisions happened before recording began, so the earliest ancestors are named but never seen.
• It shows nuclei, not cells: no membranes and no cell shapes, so a tissue reads as loose beads rather than a surface.
• It has no scale. Positions and sizes are in voxels of a recording that declares no physical size.
• The positions are the atlas’s curated tracking. We did not re-check them against the images.
• Fates are the parts list’s vocabulary, written for anatomists, and 553 of the final 580 cells carry one.
• Embryo makes no new biological claim. It is a small part of what the WormGUIDES atlas already shows, made reachable in a browser.
• One published build at a time. Build a829bdbfd6c7 is the current one; earlier builds are not kept online.