We are a group of 5 French students in engineering and we are working on a project about bacteria recognition. We chose the Fiji application to make analyses on microscope pictures for its simplicity and free availability. We are not that experienced with the imageJ application but we tried several plugins to detect the different bacteria but it’s not really efficient. Actually, we tried the shape filter plugin and the colony counter plugin which are helpful for saving the characteristics of the bacteria on a particular picture, but it’s almost useless to use these characteristics on other pictures to detect bacteria. We tried also to dilate and then use the “fill holes” option, but this method make the picture lose information so it does not work perfectly.
I included a picture to give you an example. There are seven bacteria at the top center of the picture and just one at the bottom center.
I would like to know your opinion about our problem and eventually if you have any suggestions for us, we would be glad to hear it !
Thank you so much for your answers !