Laboratoire RDP » Biophysics Team » FLORIVAR

*Table of contents*

{{TOC}}

h1. image2geometry

Pipeline to detect, orient and measure sepals

h2. 1. Preliminary : changing image formats

You will need to change different image file formats .tif format. To achieve this, you have suitable ImageJ macros in this repository's _bin/ImageJ_ folder : lif2tif, lsm2tif, inr2tif, tif2tif.

*Install the macro*: ImageJ → Plugins → Macros → Install → macroname.ijm

*Usage*: Their usage is the same. Lounch the macro and select the directory, where the files to transform are ; a new directory with the output tif files is created.

h2. 2. Normalise images

<pre> normalise.py imagefolder 30 </pre>

imagefolder=folder containing the images to normalise (.tif format)

30=common Otsu value

h2. 3. Detect the contour

The followings are different possibilities. Choose your favorite detection method and apply it on your normalised images.

h3. 3.1. By a threshold

h3. 3.2. Using the EdgeDetect of MorphoGraphX (mgx)

h3. 3.3. By the level set method (lsm)

cd in the directory with the smoothed tif files

<pre>

lsm-contour_mp.py imagefolder

</pre>

h3. 3.4. 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)

<pre>

lsm-contour_mp-from-init.py imagefolder initcontourfolder

</pre>

detected contours are written in the folder « contours »

h2. 4. Orient sepals

cd in the folder containing the contours folder and type

<pre>orient_sepals.sh contours filetype</pre>

contours = folder name containing the contours

filetype = '.tif' or '.inr.gz'

the oriented sepals are written in the "contours_oriented" folder

h2. 5. Do measurements

detected contours are in the folder « contours »

cd in the folder containing the oriented contours and type

<pre>measure_sepals.py foldername filetype</pre>

foldername = folder name containing the oriented contours

filetype = '.tif' or '.inr.gz'

the measurements are written in the "foldername_measures.csv" file