Table of contents
Pipeline to detect, orient and measure sepals. The pipeline is based on different type of scripts that we developed and can be found in this repository.
- image type transformations are done with ImageJ macros
- python scripts making use of MorphoGraphX
- python scripts that make use of TimageTk
1. Preliminaries¶
You will need to change different image file formats to .tif format. For this purpose, you have suitable ImageJ macros in this repository's bin/ImageJ folder : lif2tif, lsm2tif, inr2tif, tif2tif. 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.
Recall how to install a macro in ImageJ: Plugins → Macros → Install → macroname.ijm
2. Normalise images¶
usage: normalise.py imagefolder 30
positional arguments:
imagefolder folder containing the images to normalise (.tif format)
30 common Otsu value
3. Detect the contour¶
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 some clicks on MorphoGraphX:
-> Process -> System -> set current stack -> Both + double click on Set current stack
4. Orient sepals¶
cd in the folder containing the contours folder and type
usage: orient_sepals.sh contours filetype
positional arguments:
contours folder name containing the contours
filetype '.tif' or '.inr.gz'
the oriented sepals are written in the "contours_oriented" folder
5. Do measurements¶
5.1. All but area measurements¶
detected contours are in the folder « contours »
cd in the folder containing the oriented contours and type
usage: measure_sepals.py foldername filetype
positional arguments:
foldername folder name containing the oriented contours
filetype '.tif' or '.inr.gz'
the measurements are written in the "foldername_measures.csv" file
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 one csv file per sepal containing the surface areas are saved.
5.3. Gather all geometrical measurements in one file¶
usage: gather_data.py measures_filename areadir
positional arguments:
measures_filename the outputfile at 5.1
areadir directory with area measurement outputs (output of 5.2)