Here is our recommendation how to organize the training data. Instead of copying your images and box files directly into train_images / train_annot, you can copy them into subfolders. One for each data collection:
The train_image_folder and train_annot_folder parameters in the crYOLO configuration file (e.g. config.json) still point to the root directories train_images and train_annot respectively. The parameter anchors should be set roughly to the average of all particle box sizes. Other than that, the training of a general model does not differ from training a model from scratch.