Talk:ILP2006 - Carnegie stage Animations

Original web page - original page

Artistic Licence

In structures which needed to be broken up into smaller structures, to ensure the overall complex tissue was continuous with all it parts, the separate parts were traced such that they overlapped with each other. For example, in the aorta, the point where the left and right aortae fuse, Slice28, was traced in this was. The left side and part of the right side was traced with "left aorta.xdv", the right side and part of the left side was traced with "right aorta.xdv", and both fusing structures were completely traced in "joined aorta.xdv". This ensured that the right and left aortae looked completely fused as the "joined aorta.xdv" tracings series continued downwards.

Artistic Licences List

The following list outlines the various objects that were traced in Winsurf and their final filename, in Winsurf‚Äôs native XDV format. Underneath is a description of any artistic licence that was taken with regards to this structure and the slices to which the artistic licences applied.

Artistic Licences List: Pig Embryo

Pharyngeal Arches

1st pharyngeal arch left.xdv

In slides 8 and 9 the borders were somewhat abruptly ended. Also, the mandibular and maxillary portions weren‚Äôt entirely distinguishable, so primarily the mandibular part was traced, with the maxillary part included in the forbrain epidermis.xdv.

1st pharyngeal arch right.xdv

Only the mandibular part was traced, similar to the above, with maxillary included with forebrain epidermis.xdv

2nd pharyngeal arch left.xdv

In slice 7, one side of the arch was ended abruptly - this slice was included in epidermis.xdv. Also, there was some overlap with other arches from slice 9 onwards

2nd pharyngeal arch right.xdv

Similar to the above, overlap with other arches

3rd pharyngeal arch left.xdv

In slice 7 a small area was traced to keep continuity with the rest of the epidermis. Again there was pharyngeal arch overlap. Also, the arch‚Äôs position in slice 11 was approximated as the boundaries were unclear.

3rd pharyngeal arch right.xdv

Similar to the 3rd pharyngeal arch left.xdv, a small area was traced in slice 7, although it was more distinctly recognizable as part of the arch. The arch‚Äôs position in slice 11 was even more approximated that the left arch. Once again, there was arch overlap.

4th pharyngeal arch left.xdv

The position was approximated in slice 9, based on knowledge of the location of the arch artery; it was also approximated in slice 11. Part of the arch was included with the epidermis, in earlier slices.

4th pharyngeal arch right.xdv

Position was approximated in slice 8 and slice 11. Arch overlap occurred.

Gastrointestinal Tract

allantois.xdv

The tracing in slice 37 was enlarged and lengthened to allow for more accurate interpolation with slice 36

duodenum.xdv

The duodenum was traced larger than it ought to be, to ensure continuity with the stomach.

gallbladder.xdv

No licence taken

hindgut.xdv - is actually only half of the hindgut, from the point where it begins to move towards the tail of the embryo

No licence taken - although despite the name, it is only half the hindgut

liver.xdv

No licence taken

lower stomach.xdv

Mostly a tracing over the greater omentum, to make the stomach appear complete, as the junction between the upper and pyloric portions of the stomach

midgut.xdv

Parts were not traced to ensure interpolated continuity

oesophagus.xdv

In slice 23, the size was increased to smooth the transition with it and the stomach

oropharyngeal membrane.xdv

Completely approximated in slice 8 and combined with the pharynx in slice 9

pharynx.xdv

Some licence taken in slice 8

pyloric part of stomach.xdv

No licence taken

stomach.xdv - the remaining, untraced parts of the stomach

No licence taken

upper hindgut.xdv - the portion of the hindgut before it begins to move to the tail of the embryo

As the structure was not cut continuously, there are slices where it enters more than once. To ensure continuity, parts of it were not traced

Nervous System

forebrain.xdv

The forebrain was traced as it appeared, although when necessary the joined sections between it and the optic vesicles were traced.

hindbrain.xdv

The border between the hindbrain and midbrain was estimated and placed in the approximate area

left/right optic vesicle.xdv

No licence for right vesicle; in slice 2 the boundary of the left vesicle was approximated, as it joined with the forebrain

midbrain.xdv

The border between the midbrain and hindbrain was approximated

notochord.xdv - the part of the notochord prior to where it moves to the tail of the embryo

Part in slice 47 was not traced to ensure continuity between notochord and notochord tail.xdv

notochord tail.xdv - the part of the notochord continuous with the tail of the embryo

In some slices, its position was approximated

spinal cord.xdv - the part of the spinal cord prior to where it moves to the tail of the embryo

Part not traced in slice 47 to ensure interpolation continuity

spinal cord tail.xdv - the part of the spinal cord continuous with the tail of the embryo

No licence taken

Circulatory System

arch artery 1 left.xdv - pharyngeal arch artery

In slice 11, the artery was traced as though it were leaving the aortic sac, although the actual artery could not be found on the slice. This was to ensure that the artery was connected to the sac. The artery was randomly added to slices until slice 7 when it was visible. The invisibility of the artery could be an artifact caused by the sectioning.

arch artery 1 right .xdv - pharyngeal arch artery

Very similar to arch artery 1 left.xdv except the artery was never visible.

arch artery 2 left .xdv - pharyngeal arch artery

In slice 7 the artery was visible but only the centre was traced, else interpolation wasn‚Äôt correctly occurring. For the rest of it, the artery was barely visible, with the tracings making it enter the aortic sac.

arch artery 2 right .xdv - pharyngeal arch artery

In slice 6, the diameter of the artery was enlarged for interpolation. The artery couldn‚Äôt be seen for most of the sections, and was made to join the aortic sac.

arch artery 3 left .xdv - pharyngeal arch artery

No licence taken

arch artery 3 right .xdv - pharyngeal arch artery

Once again the location wasn‚Äôt always clear. It was made to join the aortic sac

arch artery 4 left .xdv - pharyngeal arch artery

No licence taken

arch artery 4 right .xdv - pharyngeal arch artery

In slices 9 and 10 the artery was somewhat visible, in 11 it was made to join the aortic sac, in 8 and 7 it was made to join the right aorta

ductus venosus.xdv

The structure was only traced in slice 29 and slices 26-23. It was only visible in 29 - for the other slices it was estimated and traced at its position inside the liver

heart.xdv - not a tracing of the complete heart, just those parts which weren‚Äôt traced as separate objects

No licence taken, although obviously it‚Äôs not a tracing of the complete heart. The rest was completed in separate objects, as was the internal structure of the heart.

joined aorta.xdv - the aorta, after fusion of the left and right aortae, to the point where it moves to the tail

No licence taken

joined sinus venosus.xdv - the part of the sinus venosus not already traced in other objects

No licence taken, although the structure split in two in slice 22 but there was no need to create a 2nd object

left/right anterior cardinal vein.xdv

With both veins, the end of the vein was extended so that they terminated towards the forebrain side of the embryo

left/right aorta.xdv - the aorta, before fusion to form the joined aorta

No licence taken

left/right common cardinal vein.xdv

No licence taken

left/right common iliac artery.xdv - from the bifurcation of the aorta

No licence taken

left/right hepatocardiac channel.xdv

In both cases, the channel‚Äôs position was estimated within the liver and made to join the sinus venosus

left/right sinus venosus.xdv

No licence taken

left/right posterior cardinal vein.xdv

No licence taken

left/right umbilical artery.xdv - the part of the umbilical artery before it moved towards the tail

In both cases much data was missing, however the left was missing less i.e. was visible in more slices. Based on the limited information, the location of both arteries was approximated

left/right umbilical artery tail.xdv ¬≠- the part of the umbilical artery in the tail of the embryo

The left had no licence taken; the data for the right was missing but could be approximated as a limited amount was available.

left/right umbilical vein.xdv¬≠ - the umbilical vein before it moves towards the tail

In both cases, the point where they entered the liver was approximated

left/right umbilical vein tail.xdv - the umbilical vein in the tail of the embryo

The left was visible in all slices but 32; the right was mostly not visible and had to be approximated

left/right ventricle.xdv - part of the heart

No licence taken

lower left atrium.xdv - part of the heart

The lower part of the left atrium - the rest was in the heart.xdv. No licence taken

pericardium.xdv - part of the heart

No licence taken

right vitelline vein.xdv

As the structure was split, parts of it were not traced to ensure interpolated continuity between the parts that were

tail aorta.xdv¬≠ - the part of the aorta where it moves to the tail of the embryo

No licence taken

truncus arteriosus.xdv

In some slices, was not clearly visible, so was approxiamted

upper left/right atrium.xdv - part of the heart

No licence taken

Surface

caudal end.xdv¬≠ ¬≠- the portion of the epidermis below the heart bulge

No licence was taken, except at the umbilical cord and the area below it, to ensure smooth interpolation

forebrain epidermis.xdv - the part fo the epidermis that covers the forebrain, anterior to the pharyngeal arches

There was some overlap with the 1st pharyngeal arch.xdv, as the forebrain epidermis included the mandibular part of the arch.

heart bulge.xdv¬≠ - the part of the epidermis that overlies the heart

In slices 10 and 11, some overlap occurred with the 4th pharyngeal arches.

tail.xdv - the tail of the epidermis, until it joins the caudal end of the epidermis

In slice 31 onwards, the missing right side of the tail surface was approximated

Genitourinary

cloaca.xdv

No licence taken

left/right combined mesonephros.xdv - a joining section between the body and tail mesonephros. Also contains the mesonephros in the embryo‚Äôs rump

Defines the part of the mesonephros that is the combination of the tail and body mesobnephros
In both, to get the convoluted look of the mesonephros, data points were added in the inner surface, with some attempt made to roughly trace some of the internal labyrinth - however, the tracing wasn‚Äôt hugely accurate

left/right mesonephric duct.xdv - the part of the mesonephric duct before it moves towards the tail

Sometimes difficult to determine its position in the mesonephros - was estimated in these cases (only a few times). Doesn‚Äôt include the part of the duct in the tail

left/right mesonephric duct tail.xdv - the part of the mesonephric duct contained in the tail

No licence for the left tail duct; the right duct had to be estimated in slides 35-33, due to missing data

left/right mesonephros.xdv - the mesonephros, in the mid-embryo, before it becomes the combined mesonephros

Similar to the combined mesonephros, was traced to highlight its convoluted nature

left/right tail mesonephros.xdv (error: left is called "left tail metanephros.xdv") - the mesonephros in the tail region of the embryo

Initially both were traced where the mesonephric duct was in the end of the tail (from slice 32 downards). As they grew larger, the convoluted nature was similarly traced as in the mesonephros and combined mesonephros

urogenital sinus.xdv

Made to eventually join the allantois

Respiratory System

left/right lung bud.xdv

No licence was taken for the right lung bud; however the left lung bud was approximated as it could not be seen

trachea.xdv

No licence taken

Artistic Licences List: Human Embryo

Circulatory System

aorta.xdv - the complete aorta, except without the ascending aorta, from the heart. Continues down till its bifurcation

In slices 22 and 23, parts of the aorta were not traced, to allow for better continuity with the ascending aorta

ascending aorta.xdv¬≠ - the remainder of the aorta, from the heart till the aortic arch

No licence taken

azygos vein.xdv

Made to join the IVC and SVC

basilar artery.xdv

No licence taken

brachiocephalic trunk.xdv

No licence taken

ductus arteriosus.xdv

Was not clearly visible - needed to be approximated and connected between aortic arch and pulmonary trunk

heart.xdv - not the complete heart, just the remainder, what was not traced separately

No licence taken

inferior vena cava.xdv

No licence taken

left/right atrium.xdv - part of the heart

No licence taken

left brachiocephalic vein.xdv

No licence taken

left/right common carotid artery.xdv

No licence taken

left/right common iliac artery.xdv

No licence taken

left/right common iliac vein.xdv

Not always visible - was approximated in some slices

left/right external carotid artery.xdv

No licence taken

left/right internal carotid artery.xdv

No licence taken

left/right pulmonary artery.xdv

No licence taken

left/right renal artery.xdv

Not at all visible, was approximated and added in

left/right renal vein.xdv

Not at all visible, was approximated and added in

left/right thymus.xdv - the lobes of the thymus

No licence taken

left/right ventricle.xdv - part of the heart

No licence taken, however the tracing is not of the complete ventricle of the heart, only part of it

left/right ventricular wall.xdv - part of the heart

The boundaries of the walls were estimated; areas were left for the aorta and pulmonary trunk

left/right vertebral artery.xdv

No licence taken

pulmonary trunk.xdv

No licence taken

superior vena cava.xdv

No licence taken

umbilical vein.xdv

Was made to join the ductus venosus

Gastrointestinal Tract

duodenum.xdv - a continuation of the stomach

No licence taken

hindgut.xdv

In slice 39, part was not traced to retain interpolation continuity

jejunum ascending.xdv - part of the jejunum, continuous with the duodenum

No licence taken

jejunum descending.xdv - part of the jejunum

No licence taken

larynx.xdv - part of the larynx, not the complete structure. Basically the lumen, to show its continuity with the pharynx

Needed to be approximated in slice 14, as it was not visible, and slice 18 where part of the epidermis was missing, along with the trachea

left/right liver lobe.xdv - part of the liver

In some slices, the boundary between the left and right lobes needed to be approximated

liver.xdv - the remainder of the liver

No licence taken, although is not the complete tracing of the liver

midgut caudal loop.xdv - the part of the midgut leading to the umbilical herniation

No licence taken

oesophagus.xdv

No licence taken

pancreas.xdv

No licence taken

pylorus.xdv - part of the stomach

In slices 37 and 38, the boundaries between the pylorus and the rest of the stomach were approximated

rectum.xdv - continuous with and part of the hindgut

No licence taken

stomach.xdv - the remainder of the stomach, that was not previously traced

In slice 37, its boundary with the pylorus was approximated, as the pylorus was treated separately

umbilical cord hindgut.xdv - the end of the umbilical herniation, which returns to the embryo

No licence taken

umbilical intestine #.xdv (1-11) - various parts of the umbilical herniation

It was never clear where the various parts of umbilical herniation joined in various slices. Thus, parts were carefully combined to make a complete continuous structure. Not all sliced areas through the herniation were joined together - some areas were not traced.

Genitourinary System

bladder.xdv - continuous with the urethra

Also includes the urachus. Some licence was taken to make this connect to the umbilical herniation - the urachus was estimated so that it connected with herniation

left/right adrenal glands.xdv

No licence taken with the right adrenal gland. The left adrenal gland was somewhat enlarged into the metanephros to preserve the continuity of the interpolation

left/right gonad.xdv

No licence taken

left/right mesonephric duct.xdv

No licence taken

left/right mesonephros.xdv

No licence taken

left/right metanephros.xdv - the kidneys

No licence taken with the left. With the right though, to make the structure more recognizable, and improve its continuity with the adrenal gland, an extra approximate tracing was performed in slice 35, where the adrenal gland is.

left/right paramesonephric duct.xdv

No licence taken

left/right ureter.xdv

Was made to join the point where the metanephros had a gaping hole; some of the earlier slices were unclear

urethra.xdv - continuous with the bladder

No licence taken

Skeletal System

cervical vertebra # left/right.xdv (1-4)

For these and all the vertebrae, the general shape of the vertebrae was approximated for all the vertebrae. Also, all the vertebrae traced in 2 slices, meaning that there was no space between the vertebrae (so the intervertebral discs or other features were never traced)

left/right clavicle.xdv

The end was made to join the sternum

left/right femur.xdv - part of the femur, not a complete tracing

The outer area of the structures were somewhat ignored and the structures were traced as two-part structures to preserve the continuity of the interpolation

left/right femur head.xdv - the head of the femur

Tracings included the area missed in the above structure. On both sides, the tracing was extended to a slice below where it ended, to more appropriately portray the entire femur.

left/right humerus.xdv

No licence taken

left/right ilium.xdv

In slice 47, only half of the structure was traced in both sides, as it combines at this point with the ischium

left/right ischium.xdv - part of the ischium

In slice 47, the structure was completely traced, on both sides, to improve its continuity with the ilium

left/right ischium curve.xdv - the remainder of the ischium, which joined the pubic symphysis

This structure was not at all visible - it was merely added by tracing a structure that combined part of the pubic symphysis with the ischium, on both sides of the embryo

left/right pubis.xdv

In slice 45, both left and right were extended to improve continuity with other elements of the skeletal system, and interpolation. In slice 47, only half of the acetabulum was included in the trace, as this is where the pubis meets the ilium and ischium

left/right scapula.xdv

No licence taken

meckels cartilage left/right.xdv

In slice 14, both sides were extended laterally to allow better interpolation

pubic symphysis.xdv

No licence taken

sternum.xdv

At times the boundaries were unclear and had to be approximated

vertebra # left/right.xdv (1-28)

Identical to how the cervical vertebrae were traced. For these and all the vertebrae, the general shape of the vertebrae was approximated for all the vertebrae. Also, all the vertebrae traced in 2 slices, meaning that there was no space between the vertebrae (so the intervertebral discs or other features were never traced)

Surface

epidermis.xdv

Licence was taken in a variety of places. A number of the images were missing some ends of the embryo surface, which needed to be approximated. Also, the boundaries between the body and the lower/upper limbs, and the umbilical cord were approximated

left/right lower limb.xdv

The boundary between the limb and the rest of the body needed to be approximated. Also, in the right limb, a discontinuity was seen in slice 47 and licence was taken to rectify this

left upper limb proximal.xdv/ right upper limb.xdv

Due too excessive missing data, a boundary was drawn where the limbs were cut off, allowing complete depiction of the length of the humerus bones, but no further

umbilical cord.xdv

The umbilical cord had been cut at a certain point in all the slices - it could be traced not further than that

Respiratory System

left/right arytenoid cartilage.xdv - part of the larynx

No licence taken

left/right cricoid cartilage.xdv - the lower part of the larynx

In slice 18, part of both sides of the structure were missing and had to be approximated

left/right lung.xdv

No licence taken

left/right thyroid cartilage.xdv - the upper cartilage of the larynx

No licence taken

left/right thyroid gland.xdv

No licence taken

right main bronchus.xdv - bifurcates from the trachea, the left is more vertical, and so was made continuous with the trachea

No licence taken

pharynx.xdv

In slices 12 and 13, the pharynx was approximated as the boundaries weren't clear

tongue.xdv

In slice 13, the boundary was unclear and had to be approximated

trachea.xdv - becomes the left main bronchus

In slice 18, the trachea was missing and had to be approximated

Central Nervous System

left/right cerebellum.xdv

Some overlap with the metencephalon

left/right diencephalons.xdv

In slices 2-4, where it was surrounded by other components of the CNS, the boundaries were unclear - the boundaries needed to be approximated.

left/right eye cornea.xdv - part of the eye

No licence taken with the right, but the left required some editing as the cornea was not visible in enough slices

left/right eye lens.xdv - part of the eye

No licence taken

left/right eye retina.xdv - part of the eye

No licence taken

left/right eye sclera.xdv - part of the eye

No licence taken - was made partially transparent though

left/right lower pons.xdv

In slice 8, the pons were approximated, within the metencephalon

left/right medulla.xdv

No licence taken

left/right mesencaphelon.xdv

From slice 2-4, the boundaries of the mesencephalon were unclear, as it was surrounded by other CNS components. Its boundaries were approximated for both the left and right sides.

left/right neocortex.xdv

This was a complex structure as it started off as closed structures that opened into the developing ventricles. As such, both the inner and outer borders were traced as a single object for both sides. Then, in slice 3, when the structure opened up, the structure was traced as a single object, for both left and right sides.

left/right optic nerve.xdv

Both nerves only appeared in slice 8. They were both approximately traced also in slice 7 so that the structure could be interpolated (interpolation cannot occur with a single slice). Additionally, only parts of the structure were visible in slice 8, however it was traced as a continuous nerve.

left/right outer neocortex.xdv

The boundaries of both sides were approximated

left/right upper pons.xdv

For the length of the structure, its boundaries had to be approximated as it was difficult to distinguish from it and other CNS structures

spinal cord.xdv

The spinal cord was traced as a two-part structure, with it and the central canal. Also, in slices 26, 48 and 49 it was partly missing and needed to be approximated

The Making of the Models

Please note that the images shown below have been simplified and the number of slices shown in each has been dramatically decreased for ease of understanding.

As stated, the models were generated using the serial slices available here. The serial slices were produced by sectioning the embryo into separate slices and subsequently mounting each slice for viewing under a high power microscope. These were then scanned and digitally edited to remove any distortion or artifacts that may have been generated. The adjacent image

shows sectioning of the pig embryo. An unavoidable result of the sectioning is that some data from the top and bottom of the embryo can not be captured. For this reason, the final models are missing data in the head and rump region, giving them a "box-like" shape.

Production of the models required the use of software that was capable of converting the sectioned histological data into 3D coordinates. After thorough testing, the software package "Winsurf" or "SurfDriver" was selected. The scanned histological slices were loaded into Winsurf. Sequential data points were traced around each structure, through every slice that it was visible in. The image below shows the tracing of the epidermis of the pig embyro. The green border that forms around each slice is the final series of data points that will be utilized to generate the final model.

Once the structure has been traced in every slice it appears in, the slices need to be aligned and spaced evenly. Winsurf then takes the data that has been traced and uses it to estimate the missing information between the slices. The position of the structure in the space between two slices is approximated based on the known coordinates from the slices themselves, and this process occurs between every slice, generated a 3D representation of the original structure. In the adjacent image we can see that process occurring for the epidermis of the pig embryo. First the slices containing the epidermis of the pig embryo are aligned and accurately spaced. Finally, we see a "skin" being added over the slices as the gaps are estimated and the final epidermis is generated.