Laboratoire RDP » Biophysics Team » FLORIVAR

*Table of contents*

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h1. image2geometry

Pipeline to detect, orient and measure sepals

h2. 1. Preliminaries

You will need to *change different image file formats to .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)

Use the MGX_EdgeDetect.py script on MorphoGraphX:

- open the script file with a texteditor;

- put the path to the directory of grey sepal images (line 13)

- save the script file

- drag and drop the script file on the MorphoGraphX black window

Remark: Before you lounch the scrcipt the first time in a session, you need to do a click-combinations on MorphographX (-> Process -> System -> set current stack -> Both + double click on Set current stack)

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

h3. 5.1. All but area 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

h3. 5.2. Area measurements

Use the MGX_CurvatureMapSegmentation.py script on MorphoGraphX:

- open the script file with a texteditor;

- put the path to the directory of sepal contours (line 13)

- save the script file

- drag and drop the script file on the MorphoGraphX black window

The segmented meshes (abaxial and adaxial surfaces are treated as cells) as well as a csv file/sepal containing the surface areas are saved.