You'll find below a presentation by the author, a step-by-step installation and an example.
¶ Presentation by the author
¶ Installation
¶ Inkscape
Download and install inkscape (1.3 works fine for me)
¶ ImageJ
Download (1.54 works fine for me) and unzip (C:\ImageJ)
¶ Seaborn
Seaborn is a python package that you will install in a virtual environment (made via conda).
It's based on matplotlib (another python package), just a simpler version of it!
mamba is a "layer" on top of conda. You can simply replace mamba with conda in the lines below if you don't have it installed (or install it following these instructions )
mamba create -n seaborn
...
mamba activate seaborn
mamba install seaborn -c conda-forge
...
mamba deactivate
Your environment should be located in ˋpath_to_your_conda_envsˋ (for example users/.conda/envs/ or something you defined yourself )
You will need to specify this later :
- path_to_your_conda_envs\seaborn\python.exe
or - path_to_your_conda_envs\seaborn\bin\python.exe
¶ Figure Extension
¶ Download
From the inkscape-imagej-panel repository download the project as a zip. You will find a inkscape-imagej-panel-master.zip in your download folder.
¶ Install
- Open Inkscape ,
- Go to Edit > Preferences ,
- Select the System tab ,
- Locate the User extensions line , click on the
Openbutton - Unzip the
inkscape-imagej-panel-master.zipin this folder - Restart Inkscape
¶ Configure ImageJ Macro Panel
In Inkscape :
- Extension > Figure > ImageJ Macro Panel
- Setup tab
- Define :
- Java Program : C:\ImageJ\jre\bin\java.exe
- ImageJ Program : C:\ImageJ\ij.jar
¶ Configure Matplotlib Panel
In Inkscape :
- Extension > Figure > ImageJ Macro Panel
- Setup tab
- Define :
- python cmd :
path_to_your_conda_envs\seaborn\python.exe
- python cmd :
¶ Example
Download the images from this zenodo repository
Download the image (svg) below that contains scripts to reproduce the results
¶ Analyse images with ImageJ to generate results.csv
The image(s) description contains the ImageJ macro code that you can use in ImageJ.
- In Inkscape:
- open the svg,
- select an image,- go to
Object > Object Properties, - copy the code from the description tab.
- go to
- In ImageJ :
- go to
Process > batch > Macro - Paste the code and simply remove the line
open(path/filename) - Define the path to the folder containing the image (link above), and a different output folder.
- RUN
- Save the results table as a csv
- go to
¶ Re-create the Figure
In Inkscape:
- open the svg,
- select an image,
- go to
Object > Object Properties - modify code as necessary (path to images)
- use the ImageJ macro panel to regenerate image
- go to
- select the graph
- modify code as necessary (path to Results.csv)
- use the Matplotlib panel to regenerate graph