Haeckaliens is a collection of 3D datasets and reconstructions of embryos obtained with the open-source optical tomography scanner "OPenT" .
What the heck are "Haeckaliens"? Haeckel was one of my "scientific heroes", and a common comment we get is that some images look like aliens....hence, Haeckaliens!*
(1874 illustration from Ernst Haeckel's Anthropogenie showing "early", "mid" and "late development" stages of several vertebrate embryos: ﬁsh (F), salamander (A), turtle (T), chick (H), pig (S), cow (R), rabbit (K), and human (M). - Source: Wikipedia). Superimposed are images of some of the embryos already imaged with OPenT and available here.
Information about imaging with OPenT and the system are at: https://sites.google.com/site/openspinmicroscopy/home/opt
We're looking for volunteers/collaborators, specimens (non-model species please!), help with sample preparation, image acquisition and 3D analysis!
Not all features are available for all specimens...it's an ongoing project!
Visitors are welcome to use images as long as they acknowledge the source.
Some instructions for using the interactive datasets in XTK format are here. For "offline rendering" you can open the TIFF datasets in FIJI/ImageJ, VolViewer, 3D Slicer, Drishti and other software. We're also working with Bitplane to provide versions that can be used with the Imaris or the Imaris SceneViewer (free; can be downloaded here).
NOTE: due to changes in dropbox and youtube we're experiencing problems with the display of the XTK and 3D youtube videos. We're working on alternatives...
If you are looking for other online developmental anatomical databases for model species I recommend the following:
ZFAP - Zebrafish Anatomy Portal: http://www.anatomyportal.org/
Quail anartomy Portal: http://quail.anatomyportal.org/
eMouse atlas: http://www.emouseatlas.org/emap/home.html
eChick atlas: http://www.echickatlas.org/ecap/eca_home.html
Amniotes (normal anatomy)
THESE ARE THE SPECIMENS WHICH WON THE NIKON SMALL WORLD CONTEST!
Specimens were provided by Rob Bryson-Richardson and the full 3D datasets are now available online through the "Quail Anatomy Portal" http://quail.anatomyportal.org/; I recommend starting with the quail staging tool: http://quail.anatomyportal.org/staging_tool.php
- Common pigeon (Columba livia)
Stage: 18 days (full gestation ~18 days)
- Duck (Anas platyrhynchos)
Stage: ~24 days (full gestation ~28 days)
- Gecko (Hemidactylus turcicus) - specimen kindly provided by Rui Castanhinha
Anamniotes (normal anatomy)
- Common toad (Bufo bufo)
Stage: hindlimb budsLength [dehydrated] = 2.97cm
XTK interactive 40umRes 3D dataset TIF.zip 20umRes dataset Sagittal sections (YouTube) Segmented anatomy (3D PDF)
- Tree frog (Hyla arborea) - specimen provided by Rui Rebelo
* see a naturally occurring mutation of this species below!
Other datasets in prep:
- Common frog (Pelophylax perezi)
- Minnow (Squalius alburnoides) - collaboration with Angela Inácio, MJ Collares-Pereira & Manuela Coelho
- Sardine (Sardina pilchardus) - specimens provided by Susana Ferreira and Pedro Ré
- Sepia (Sepia sp)
Mutants and dysmorphic embryos
- Dysmorphic Lusitanian toadfish (Halobatrachus didactylus) - Specimen provided by Paulo Fonseca.
* Before I get charred for "trying to revive the recapitulation theory", no...that is not the point of the illustration! This was one of the reasons I got into embryology and I always liked the controversy and intellectual challenge it sparked. Haeckel's "heresy" was the publication of illustrations which were often too "artistic" (there is an interesting review by Richardson et al on this theme here).