init: add note

note/note.qmd

+---
+format:
+  pdf:
+    geometry:
+      - top=5mm
+      - bottom=20mm
+      - left=25mm
+      - right=25mm
+subtitle: "Using mathematical morphology to derive physical metrics and measurements of an animal."
+title: "Image Measurement"
+---
+
+```{=latex}
+\vspace{-2.5cm}
+```
+
+## Context
+
+The data consist of a bank of pictures of Geriss (and Larva) taken at the IGFL animal facility:
+
+* format: `.JPG`,
+* dimension: $3600 \times 2400$ ($2560 \times 1920$),
+* 3 channel colors.
+
+The aim is to extract measurements of each animal in each picture using common mathematical morphology
+approaches.
+
+
+## Main steps
+
+The analysis is composed of five main steps:
+
+1. Cropping
+2. Binarization
+3. Segmentation
+4. Contour detection
+5. Morphometrics
+
+Steps 1 to 3 are performed with the R package `imageR` (close equivalent to the Python package `scikit-image`), steps 4 to 5 with R package `Momocs`.
+
+
+## Quantity of interest
+
+The measurements to extract for each animal are the following:
+
+- the body size (area of the abdomen),
+- the tibia and femur lengths of the posterior legs,
+- the sex,
+- the presence of wings.
+
+The sex and the presence of wings are respectively characterized by the lower and upper part of the body. Figure 1 highlights the difference for the sex and for the presence of wings.
+
+::: {#fig-geriss layout="[[1,1,1,1]]"}
+
+![](figures/Fig1a.png)
+
+![](figures/Fig2a.png)
+
+![](figures/Fig1b.png)
+
+![](figures/Fig2b.png)
+
+Body shape difference between sexes and presence of wings. From left to right: male no wings, male wings, female no wings, female wings.
+:::
+
+
+
+