This is a little bit late in the day to talk about this, but I've noticed that if I load black and white JPEGs like UAB236_LH into a matrix, they are actually flipped down versus the RGB images, so I have to rotate them 180 degrees to get them to same orientation. At the same time, when looking at the images with photo viewer, they all look aligned the same way. So there are some transform tags in there that Python is not sensitive to. Looking at the image data, it was processed in Photoshop. It's this: https://stackoverflow.com/questions/13872331/rotating-an-image-with-orientation-specified-in-exif-using-python-without-pil-in Never mind, just a bit of whinging on a Sunday morning. Actually skimage seems to observe the tags and do the right thing.