Tutorial for efficient and reproducible measurements in FIJI (PDF).

Tutorial on how to readout image metadata & adding a scale bar (PDF).

Tutorial (PDF) and example file.

Tutorial on generating file lists via command line (PDF)

The PDF explains how the macros listed here can be installed in FIJI.

The macro “Generate_folder_structure.py“ in FIJI generates a project folder with the subfolders: analyses_code; figure_plates; manuscript; processed_data; raw_data; readme_files & submission at a location specified by the user.

The macro „Generate_folder_and_subfolder.py“ in FIJI generates a folder with a user-defined number of subfolders at a user-defined storage location, for which the names are also queried in the macro. This allows template folders to be generated, e.g. for the organisation of project data.

The Macro „Generate_file_list_add_columns.py“ allows from FIJI to select a folder with images and create a csv file, listing the image names and add additional columns with static values. It also allows saving and loading templates (in JSON format) for such additional columns.

The script “edx_spectrum_processor.py” uses Python to read out an entire folder full of raw data of EDX point measurements (AZTEC software, Oxford) in .txt format and write it bundled into a single CSV file. The script checks for any spaces in the file name (e.g. spectrum 1.txt) and corrects them. A second CSV file is also generated, which contains the spectrum peaks automatically recognised by the software for each spectrum.  The specific file path to the folder with the TXT files and the desired folder for the output must be adjusted in the script (Line 50 & 84). The CSV files can then be used to plot the data efficiently in Python or R in a uniform standardised format (and, if desired, also label the detected elements). 

Where can I download FIJI?

The latest version for the relevant operating system can be downloaded here.

Is there a user manual for ImageJ / FIJI?

Individual tools and further information can be called up via the search window, as well as via the help function. There is also a training manual for FIJI which explains many basic functions in detail.

Is it possible to batch export images from Array Tomography (2D) sessions?

Unfortunately, this is not currently provided for in the software.