image2gometry: pipeline to detect, orient and measure sepals¶

1. ImageJ : lif2tif¶

ImageJ → Plugins → Macros → Install → lif2tif.ijm
lounch the macro and select the directory, where the lif file is ; a directory with the 2D-smoothed tif files is created.

2. normalise images¶

normalise.py 30

2. detect the contour using lsm¶

cd in the directory with the smoothed tif files

tif2contour.py 30 0.6

30=common Otsu value, 0.6 factor for thresholding
(uses normalise.py and lsm_contour_mp.py)

2bis. lounch lsm on an already prepared initial contour (mgx for instance)¶

cd the directory, which contains a directory of (normalised and smoothed) images and another with the initial contours (same filename cooresponding to the same image)

lsm-contour_mp-from-init.py imagefolder initcontourfolder

detected contours are written in the folder « contours »

3. orient sepals¶

cd in the folder containing the contours folder and type

orient_sepals.sh contours filetype

contours = folder name containing the contours
filetype = '.tif' or '.inr.gz'
the oriented sepals are written in the "contours_oriented" folder
(uses orient_sepal.py)

4. do measurements¶

detected contours are in the folder « contours »
cd in the folder containing the oriented contours and type

measure_sepals.sh foldername filetype

foldername = folder name containing the oriented contours
filetype = '.tif' or '.inr.gz'
the measurements are written in the "foldername_measures.csv" file
(uses measure_sepal.py)