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"Haeckaliens"


Brief Intro:
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 colleagues people often comment my reconstructions 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

I'm looking for volunteers/collaborators, specimens (mostly 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.
The RAW and processed datasets will be available later with DOIs hosted on Zenodo


I had some models available to view interactively in WebGL/XTK format (instruction here), but those are now broken and I am looking for an alternative. For "offline rendering" you can open the TIFF datasets in FIJI/ImageJDrishti (Rendering), 3D Slicer (segmentation) and other tools. Some of these datasets have been used by Bitplane and Aivia to demo their software, Imaris and Aivia, respectively


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 anatomy Portal: http://quail.anatomyportal.org/



Amniotes (normal anatomy)


 www.gabygmartins.info/research/haeckaliens/RabbitWithSkin.jpg
Stage: term (=mouse TS24
Full gestation = 29days
CRL [dehydrated] = 4.4cm (straightened!)

(bones)      (vessels)

Aivia rendering here
 



 www.gabygmartins.info/research/haeckaliens/CoBaiaWithSkin.jpg
Stage: unknown (=mouse TS23?) 
Full gestation ~65 days
CRL [dehydrated] = 1.6cm



 
  Post-natal: 2days
CRL (dehydrated) = 

 
 
 E18 () 
CRL (dehydrated)  = 
Sample prepared by André Dias, Imaged by Alexandre Lopes, Recosntructed by A. Lopes & GabyGMartins.
 
   
 
Stage: 14days (TS22
Full gestation = 19 days
CRL [dehydrated] = 5.8mm
 
      

      
THESE ARE THE SPECIMENS WHICH WON THE NIKON SMALL WORLD CONTEST AND OTHER THE STAGES NO INCLUDED IN THE QUAIL ANATOMY PORTAL:
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
     





Stage: 10 days 
(full gestation ~16 days)
CRL [dehydrated] = 2.3cm  

 

Stage: 13 days 
(full gestation ~16 days)

 
 

Stage: 15 days
(full gestation ~16 days)
CRL [dehydrated] = 4.2cm

 


- 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

         (stage unknown)



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



           
 Lusitanian toadfish (Halobatrachus didactylus)
 Collaboration with Paulo Fonseca, Pedro Félix, José Lino and Clara Amorim.
 
These datasets refer to a publicationFelix PM, Gonçalves A, Vicente JR, Fonseca PJ, Amorim MCP, Costa JL, & Martins, GG (2016). Optical micro-tomography “OPenT” allows the study of large toadfish Halobatrachus didactylus embryos and larvae. Mech of Develop doi:10.1016/j.mod.2016.03.001
  
Stage: 20 dpf
(hatching ~30 days)
Length [dehydrated] = 7.01 mm

 
      
Stage: 30 dpf
(hatching ~30 days)
Length [dehydrated] = 8.39 mm
 
  
Stage: 46 dpf
(hatching ~30 days)
Length [dehydrated] = 18.9 mm
 
  

 
 

 * see a naturally occurring mutation of this species below!

Stage: ~2months PF
(hatching ~30 days)
Length [dehydrated] = 20.73 mm
 


Other datasets in prep:


- Shark embryos (Colalboration with Catarina Santos e Rui Rosa - FCUL)

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

  

Invertebrates



- Sepia (Sepia sp)

    Stageundetermined 



Mutants and dysmorphic embryos


- Dysmorphic Lusitanian toadfish (Halobatrachus didactylus)  -      Specimen provided by Paulo Fonseca.
       


Stage: undetermined ~3weeks PF; 
Length [dehydrated] = 1.1cm
(SEE NORMAL EMBRYO ABOVE!)
This fish was still in the corion when collected, even though its siblings had mostly ecloded. Though the head appears to be normal, its body is severely truncated!
This, and many other abnormalities occur in this species.
       




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*  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). 

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