That is a very delicate line to walk, as journals are incredibly strict about image manipulation. You should only ever adjust the brightness and contrast globally across the entire image, never locally. If your raw data is still hard to interpret visually, sometimes it is better to pair it with a schematic drawing. I actually got this idea after seeing how Ella Maru Studio
https://scientific-illustrations.com/ balances raw data with artwork. They create clear scientific images and animations that can accompany your experimental data to show exactly what the viewer should be looking at. Placing a beautiful 3D schematic right next to your grainy microscopy slide helps the audience understand the structure instantly while keeping your original data completely untouched and honest.