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03plankton_gelatinous.qmd
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# Plankton_gelatinous
```{r setup, warning=FALSE}
source("R/init.R")
vigns <- fs::dir_ls(
here::here(training_dir, "Plankton_gelatinous"),
type = "file", glob = "*.png", recurse = TRUE)
```
## Tunicata
Tunicates are a subphylum of the Chordates. Their name comes from the tunic produced by the epidermis covering them. The larval stage of these organisms has a notochord (not present in the adult stage) [@ruppert2004].
### Thaliacea
#### Salpida {#sec-salpida}
##### salpidae
These organisms are transparent, which is indicated by the very light yellow on the vignettes. The band of muscle present in the Doliolida is not present. There is, however, the presence of muscle. The barrel shape of the Doliolida is not present. ( @sec-doliolida ).
![Vignette (A) and Image (B) of Salpida [@caicci2013].](images/03plankton_gelatinous/salpida.png){width="250"}
@fig-vig-salpidae shows several vignettes of Salpidae.
```{r}
#| label: "fig-vig-salpidae"
#| fig-cap: "Vignettes of the Salpidae"
plot_vignettes(vigns, group = "Salpidae")
```
This group is similar to the `salpida` group in ZooScanNet (@fig-zsn-salpida).
::: {#fig-zsn-salpida layout-ncol="2"}
{width="250"}
{width="250"}
{width="250"}
{width="250"}
Images of the Salpida from ZooScanNet [@elineau2018].
:::
#### Pyrosomatida
##### Pyrosomatida
::: callout-important
## New group
In previous studies (and associated training sets), this group was not studied.
:::
Pyrosomatida forms large tubular colonies several metres long. They are made up of thousands of blastozoids whose tunics are grouped together and the buccal siphon opens in the centre of the tube [@caicci2013].
![Image of the Pyrosomatida [@caicci2013].](images/03plankton_gelatinous/pyrosomatida.png){#fig-pyrosomatida}
In the ZooScanNet, they are very often found in the form of colonies (@fig-zsn-pyrosomatida). The pharynx is discernible in each image
::: {#fig-zsn-pyrosomatida layout-ncol="2"}
{width="250"}
{width="250"}
{width="250"}
{width="250"}
Images of Pyrosomatida from ZooScanNet [@elineau2018].
:::
#### Doliolida {#sec-doliolida}
These organisms have the appearance of a symmetrical barrel with a ring of several circles (@fig-doliolida). Circles are muscles surrounding the body of the organism
![Vignette (A) and image (B) of Doliolida [@caicci2013].](images/03plankton_gelatinous/doliolida.png){#fig-doliolida width="250"}
@fig-vig-doliolida shows several vignettes of Sagittoidea. These organisms are transparent as indicated by the light yellow parts on the vignettes. The muscle bands around the organisms appear darker.
```{r}
#| label: "fig-vig-doliolida"
#| fig-cap: "Vignettes of Doliolida"
plot_vignettes(vigns, group = "Doliolida", nx = 3,ny = 2)
```
This group is similar to `doliolida` in ZooScanNet ( @fig-zsn-doliolida ).
::: {#fig-zsn-doliolida layout-ncol="2"}
{width="200"}
{width="200"}
{width="200"}
{width="200"}
Images of Doliolida from ZooScanNet [@elineau2018]
:::
### Appendicularia
Appendidicularia keep their tails in the adult state. This neotenic character makes them easily identifiable. These organisms are divided into two parts: the trunk and the tail ( @fig-appendicularia ).
![Vignette of Appendicularia: A trunk B tail [@quivythomas2018].](images/03plankton_gelatinous/appendicularia_comp.png){#fig-appendicularia}
#### Copelata
##### Oikopleuridae {#sec-oikopleuridae}
The trunk is globular and all organs are tightened. The colour of the trunk is very dark. The subchordal cells arround the notochord give a dark of the tail (@fig-oikopleuridae).
![Vignette (A) and image (B) of Oikopleuridae [@hecq2014]](images/03plankton_gelatinous/oikopleuridae.png){#fig-oikopleuridae width="250"}
@fig-vig-oikopleuridae shows severals vignettes of Oikopleuridae.
```{r}
#| label: "fig-vig-oikopleuridae"
#| fig-cap: "Vignettes de Oikopleuridae"
plot_vignettes(vigns, group = "Oikopleuridae")
```
##### Fritillariidae
The trunk of these organisims is elongated. The trunk is less dense and compact than that of the OIkoploridae ( see @sec-oikopleuridae ). The colour of the tail of these organisms is rather light on the vignettes (@fig-fritillariidae).
![Vignette (A) and image of Fritillariidae [@hecq2014]](images/03plankton_gelatinous/frittillariidae.png){#fig-fritillariidae}
@fig-vig-fritillariidae shows several vignettes of Fritillariidae.
```{r}
#| label: "fig-vig-fritillariidae"
#| fig-cap: "Vignettes of Fritillariidae"
plot_vignettes(vigns, group = "Fritillariidae")
```
#### Appendicularia_tail {#sec-appendicularia-tail}
The organism is often damaged during the haul. As a result, appendicular tails are found in the samples (@fig-appendicularia-tail). There is a light band arround two dark bands [@gorsky2017].
![Vignette of the Appendicularia tail : muscle, B notochord [@quivythomas2018].](images/03plankton_gelatinous/appendicularia_tails.png){#fig-appendicularia-tail width="250"}
@fig-vig-appendicularia-tail shows several vignettes of the Appendicularia tail.
```{r}
#| label: "fig-vig-appendicularia-tail"
#| fig-cap: "Vignettes of Appendicularia tails."
plot_vignettes(vigns, group = "Appendicularia_tail")
```
This group is similar to the `tail__appendicularia` group in ZooScanNet ( @fig-zsn-appendicularia-tail ).
::: {#fig-zsn-appendicularia-tail layout-ncol="2"}
{width="250"}
{width="250"}
{width="100"}
{width="100"}
Images of Appendicularia tails fromZooScanNet [@elineau2018].
:::
## Chaetognatha
Chaetognatha are well studied pelagic predators. They are the main predators of copepods. @fig-chaetognatha shows the 3 characteristic parts of these organisms: head, trunk, tail [@pierrotsbults2017].
![Vignette of a Chaetognatha and its characteristics: head (A), trunk (B), tail (C) and hooks (D)[@quivythomas2018].](images/03plankton_gelatinous/chaetognatha.png){#fig-chaetognatha}
Fins are used to determine the species of chaetognaths [@pierrotbults2020]. The image analysis used to obtain the thumbnails does not allow sufficient accuracy of the fins to be maintained [@dugauquier2019].
### Sagittoidea
Phragmophora are distinguished from Aphragmophora by the presence of transverse musculature and abundant glandular structures on the body surface. @dugauquier2019 further classified into Krohnittidae, Sagittidae and Eukrohniidae (see [@dugauquier2019a] ). This discrimination is complex on the basis of vignettes.
@fig-vig-sagittoidea shows several vignettes of Sagittoidea.
```{r}
#| label: "fig-vig-sagittoidea"
#| fig-cap: "Vignettes of Chaetognatha"
plot_vignettes(vigns, group = "Sagittoidae")
```
This group is similar to `chaetognatha` in ZooScanNet ( @fig-zsn-chaetognatha ).
::: {#fig-zsn-chaetognatha layout-ncol="2"}
{width="250"}
{width="250"}
{width="100"}
{width="100"}
Images of Chaetognatha [@elineau2018].
:::
### Chaetognatha_head {#sec-chaetognatha-head}
::: callout-important
## New group
In previous studies (and associated training sets), this group was not studied.
:::
During sampling, these organisms can be divided into fragments. The head is separated from the trunk and the tail ( @fig-zsn-chaeto-head ). This group includes the heads of the organisms named \`head\` in the ZooScanNet [@elineau2018].
::: {#fig-zsn-chaeto-head layout-ncol="2"}
{width="200"}
{width="200"}
{width="200"}
{width="200"}
Chaetognatha head images from ZooScanNet [@elineau2018].
:::
### Chaetognatha_tail {#sec-chaetognatha-tail}
::: callout-important
## New group
In previous studies (and associated training sets), this group was not studied.
:::
During sampling, these organisms can be divided into fragments. The head is separated from the trunk and the tail ( @fig-zsn-chaeto-tail)
In ZooScanNet the group that includes chaetognatha tails is called `tail__chaetognatha` [@elineau2018].
::: {#fig-zsn-chaeto-tail layout-ncol="2"}
{width="250"}
{width="250"}
Images of Chaetognatha tail from ZooScanNet [@elineau2018]
:::
## Ctenophora
::: callout-important
## New group
In previous studies (and associated training sets), this group was not studied.
:::
The anatomical particularity of this group is the presence of 8 combs (bands composed of cilia) which allow the locomotion of the organism. These longitudinal bands are symmetrical all around the organism. This group is a rare group with a very limited number of images 39 in the ZooScanNet [@elineau2018].
## Cnidaria
### Scyphozoa
Schyphozoans are commonly known as jellyfish. These organisms are both benthic and pelagic [@licandro2017]. The successive stages of jellyfish development are presented below.
![Life cycle of Catostylus mosaicus (Scyphozoa: Rhizostomeae) [@pitt2000].](images/03plankton_gelatinous/scyphozoa_life_cycle.png){fig-align="center" width="348"}
#### Scyphozoa_ephyra
The ephyra stage is easily recognized by its 8 symmetry ( @fig-vig-ephyra ). The radial and adriatic canals are darker in the vignettes. The morphology of the radial and adriatic canals can be used to refine the classification. However, we will not go any further in this book.
```{r}
#| label: "fig-vig-ephyra"
#| fig-cap: "Vignettes of ephyra larva"
plot_vignettes(vigns, group = "Scyphozoa_ephyra")
```
This group is similar to the `ephyra` group in ZooScanNet (@fig-zsc-ephyra).
::: {#fig-zsc-ephyra layout-ncol="2"}
{width="162"}
{width="158"}
Image of ephyra larva from ZooScanNet [@elineau2018].
:::
#### Scyphozoa_medusa
In the medusa stage, the symmetry of 8 is less marked. The individual canals are always larger than in the ephyra stage. The organisms are generally larger than those of the ephyra stage (@fig-scyph-medusa).
{#fig-scyph-medusa width="285"}
@fig-scyph-medusa shows several vignettes of `Scyphozoa`.
```{r}
#| label: "fig-vig-medusa"
#| fig-cap: "Vignettes du stade méduse des Scyphozoa"
plot_vignettes(vigns, group = "Scyphozoa_medusa", nx =2, ny = 2)
```
This group is similar to the `scyphozoa` group in ZooScanNet ( @fig-zsn-scy-medu ).
::: {#fig-zsn-scy-medu layout-ncol="2"}
{width="250"}
{width="250"}
{width="250"}
{width="250"}
Image of Scyphozoa from ZooScanNet [@elineau2018]
:::
### Hydrozoa
#### Leptothecata
##### Campanulariidae
###### Obelia
::: callout-important
## New group
In previous studies (and associated training sets), this group was not studied.
:::
In the centre, the mouth of the organism is connected by radial canals to the gonads. The circular canal and the tentacular bulbs are marked at the base of the tentacles ( @fig-obelia ) .
![Image of *Obelia* sp [@hecq2009]](images/03plankton_gelatinous/obelia.png){#fig-obelia width="301"}
This group is similar to the `obelia` group in ZooScanNet ( @fig-zsn-obelia ).
::: {#fig-zsn-obelia layout-ncol="2"}
{width="200"}
{width="200"}
{width="200"}
{width="200"}
Image of *Obelia* from ZooScanNet [@elineau2018].
:::
#### Siphonophorae
Les siphonophores sont une colonie d'individus que l'on nomme zoïdes. On discrimine différent zoïdes par rapport à leur fonctions nectophore (locomotion), gastrozoïde ( digestion), pneumatophore (flottaison) [@licandro2017a].
##### Abilidae
Les abylidae ne possèdent pas de nectophores tout comme les Diphydae.
###### Abylopsis_tetragona_eudoxie
La @fig-aby-eudoxie présente sur la partie supérieur ce que nous classons dans la catégorie `Abylopsis_tetragona_eudoxie` et la partie inférieur `Abylopsis_tetragona_gonophore` .
![Eudoxie d' *Abylopsis tetragona* ( [@hecq2009])](images/03plankton_gelatinous/abylopsis_eudoxie.png){#fig-aby-eudoxie width="250"}
La @fig-vig-aby-eudoxie présente plusieurs vignettes du stade eudoxie d'*Abylopsis tetragona* (partie bractée). La forme pentagonale est très marquée ainsi que les gastrozoides plus denses sur les vignettes.
```{r}
#| label: "fig-vig-aby-eudoxie"
#| fig-cap: "Vignettes du stade eudoxie d' *Abylopsis tetragona*."
plot_vignettes(vigns, group = "Abylopsis_tetragona_eudoxie")
```
Ce groupe est similaire au groupe `eudoxie__Abylopsis_tetragona` dans le ZooScanNet ( @fig-zsn-eudoxie-abylopsis ). Les deux premières images comprennent uniquement la partie bractée de l'organisme alors que les deux suivantes proposent la partie bractée et le gonophore.
::: {#fig-zsn-eudoxie-abylopsis layout-ncol="2"}
{width="250"}
{width="250"}
{width="247"}
{width="250"}
Image d'eudoxie d' *Abylopsis tetragona* du ZooScanNet [@elineau2018].
:::
###### Abylopsis_tetragona_gonophore
La partie inférieur de la @fig-aby-eudoxie présente les gonophores d'une forme de prisme rectangulaire. La @fig-vig-aby-gonophore présente plusieurs vignettes du gonophore d'*abylopsis tetragona.*
```{r}
#| label: "fig-vig-aby-gonophore"
#| fig-cap: "Vignettes de gonophore d' *Abylopsis tetragona*."
plot_vignettes(vigns, group = "Abylopsis_tetragona_gonophore", nx = 3, ny = 2)
```
Ce groupe est similaire au groupe `gonophore__Abylopsis_tetragona` dans le ZooScanNet ( @fig-zsn-nectophore-aby ).
::: {#fig-zsn-gonophore-abyl layout-ncol="2"}
{width="250"}
Image du gonophore d' *Abylopsis tetragona* du ZooScanNet [@elineau2018].
:::
###### Abylopsis_tetragona_nectophore
Plusieurs éléments sont identifiables sur le nectophore antérieur des Abylidée (@fig-aby-nectophore) :
- la forme pentagonales
- la cavité sous ombrellaire (plus grande des 3 cavités, claire sur les vignettes)
- gastrozoide (cavité la plus dense sur l'image)
- somatocyste (cavité ovale avec un petit diverticule)
![Nectophore antérieur d' *Abylidae* [@hecq2009]](images/03plankton_gelatinous/abylopsis_nectophore.png){#fig-aby-nectophore width="262"}
La @fig-vig-aby-nectophore présente plusieurs vignettes du nectophore d'*abylopsis tetragona*.
```{r}
#| label: "fig-vig-aby-nectophore"
#| fig-cap: "Vignettes de nectophore d' *Abylopsis tetragona*."
plot_vignettes(vigns, group = "Abylopsis_tetragona_nectophore")
```
Ce groupe est similaire au groupe `nectophore__Abylopsis_tetragona` dans le ZooScanNet ( @fig-zsn-nectophore-aby ).
::: {#fig-zsn-nectophore-aby layout-ncol="2"}
{width="250"}
{width="250"}
Image de nectophore antérieur d' *Abylopsis tetragona* du ZooScanNet [@elineau2018].
:::
La @fig-zsn-comp-nectophore-aby propose une organisme complet doté de son nectophore antérieur et de son nectophore postérieur
![Image du nectophore antérieur et postérieur d' Abylopsis tetragona du ZooScanNet ([@elineau2018]).](images/zooscannet/nectophore__Abylopsis_tetragona/34916284.jpg){#fig-zsn-comp-nectophore-aby width="478"}
##### Diphydae
###### Diphyidae_gonophore
La série de vignettes présente les gonophore qui sont la partie reproductrice du stade eudoxie. On retrouve une certaine ressemblance avec les gonophores d'*Abylopsis tetragona sans le* prisme rectangulaire ( @fig-vig-diphyidae-gonophore ).
```{r}
#| label: "fig-vig-diphyidae-gonophore"
#| fig-cap: "Vignettes de gonophore de Diphyidae."
plot_vignettes(vigns, group = "Diphyidae_gonophore")
```
Ce groupe est similaire au groupe `gonophore__Diphyidae` dans le ZooScanNet ( @fig-zsn-diphyidae-gonophore ).
::: {#fig-zsn-diphyidae-gonophore layout-col="2"}
{width="250"}
{width="250"}
Image de gonophores de Diphyidae du ZooScanNet [@elineau2018]
:::
###### Diphyidae_nectophore
Les nectophores des Diphyidae sont de formes coniques. Le nectosac est plus densus sur les vignettes ci-dessous. Le long du nectosac, on observe les somatocystes ( @fig-vig-diphyidae-nectophore ).
```{r}
#| label: "fig-vig-diphyidae-nectophore"
#| fig-cap: "Vignettes de nectophores de Diphyidae."
plot_vignettes(vigns, group = "Diphyidae_nectophore")
```
::: callout-note
Le ZooScanNet propose deux groupes : `eudoxie__diphyidae` et `nectophore__diphyidae` . Nous faisons le choix de les regrouper en un seul et unique groupe : `Diphyidae_nectophore` .
:::
##### Physonectae
###### Physonectae_nectophore
Ces organismes sont constitués d'un pneumatophore contrairement aux Calycophore. La forme particulière de ces organismes les rendent aisément identifiables. On observe un resserrement à la base de la colonie.
![A: Photographie \[\@pugh2016\] et B: vignette de Physonectae.](images/03plankton_gelatinous/physonectae.png){fig-align="center" width="443"}
La @fig-vig-phy-nectophore présente plusieurs vignettes du stade méduse.
```{r}
#| label: "fig-vig-phy-nectophore"
#| fig-cap: "Vignettes de nectophore de Physonectae."
plot_vignettes(vigns, group = "Physonectae_nectophore")
```
Ce groupe est similaire au groupe `nectophore_Physonectae` dans le ZooScanNet ( @fig-zsn-physonectae ).
::: {#fig-zsn-physonectae layout-ncol="2"}
{width="250"}
{width="250"}
Image de physonectae du ZooScanNet [@elineau2018]
:::
#### Trachymedusea
##### Rhopalonematidae
###### Aglaura
La @fig-vig-aglaura présente plusieurs vignettes de Rhopalonematidae. La forme assez particulière de ce genre permet de l'identifier assez aisément. La partie plus dense dans la partie supérieur de l'organisme est son estomac et les ses gonages suspendue par un pédoncule.
```{r}
#| label: "fig-vig-aglaura"
#| fig-cap: "Vignettes d'Aglaura."
plot_vignettes(vigns, group = "Aglaura")
```
Ce groupe est similaire au groupe `Aglaura` dans le ZooScanNet ( @fig-zsn-aglaura ).
::: {#fig-zsn-aglaura layout-ncol="2"}
{width="250"}
{width="250"}
Image d'Aglaura du ZooScanNet [@elineau2018]
:::