Open access publication
This full study and new workflow has been published in the open access Climate of the past journal and can be downloaded here.
New Decanter and slide guide
The DecanteurRad12x12x8.stl and Slide_guide.stl files are available here for free, and are introduced in “A new automated radiolarian image acquisition, stacking, processing, segmentation, and identification workflow” publication available here.
A minimum layer height resolution of 0.20 mm is recommended.
AutoRadio_Segmenter.ijm ImageJ plugin
The AutoRadio_Segmenter.ijm plugin (AUTOmated RADIOlarian Segmenter) is part of the AUTOmated SEGMENTER Suit. It is a free ImageJ / FIJI Plugin that is used for automated segmentation of microscope images that contain several microfossil specimens per image (FOV).
Advantages of this plugin are multiple: it is fast to proceed, can perform image processing at the same time (contrast, inversion, watershed, morphometric measurements…), and export the segmented images into a series of folders that copy the original architecture of the cores / samples folders. (see video below).
The AutoRadio_Segmenter.ijm allows the automated processing of a root folder (“Core”), containing subfolders (“Samples”) of FOV images (Fields of View, a) that will invert them, create Region of Interests (ROIs, b) for each particle and segment and save them as individual images into separate subfolders corresponding to the different “Samples” of the processed root “Core” folder.
Some additional plugins (e.g. the BioVoxxel plugin « Watershed Irregular Features ») might be needed, according to your objectives. To use it, download the .ijm file here and save it into the ImageJ/plugins folder, and it will be available to use on after restarting ImageJ.
The original version (May 2020, used in Tetard et al., submitted) of the database (17.065 images divided into 112 classes) is freely available here.
The last version (July 2020) of the database (21.749 images divided into 132 classes) is freely available here.
If you are willing to participate in the improvement of this database, if you have images of missing species, or images to add to an under-represented species, please contact us.