Schematic representation of the workflow of the Image J Plug In to quantify viral cores inside late endosomes.

(A) Each series from raw “.lif” files are extracted as single images in TIFF format to be processed. (B) Image pre-processing actions to get discriminate viral cores and late endosome components. (C) Image processing actions to isolate viral cores: segmentation and identification by ID and feature extraction. (D) Selecting viral cores through filtering actions based on a collection of morphological, geometric, statistics and intensity thresholded features. (E) Creating a composite mask combining viral cores through OR operator. (F) Processing of late endosomes applying segmentation, background correction, binary operations as “Fill holes” and morphological filtering using the “closing” operator. (G) Combining late endosomes having mean intensity values neither 0 nor 255 using the exclusive OR operator. (H) Obtaining viral cores which are located inside late endosomes using the conjunction operator AND.

(TIFF)