For people having the same issue. I found an interesting API that does data augmentation on numpy array of any channel number, can do it on multi targets, bounding boxes, masks …
import albumentations as albu
import cv2
co_aug_transforms = albu.Compose([albu.RandomSizedCrop((300, 436), 400, 940, w2h_ratio=1024/436, p=0.5),
                                  albu.Flip(),
                                  albu.ShiftScaleRotate()
                                  ])

flow = readflo(path_to_flow)
frame1 = cv2.cvtColor(cv2.imread(path_to_frame1), cv2.COLOR_BGR2RGB)
frame2 = cv2.cvtColor(cv2.imread(path_to_frame2), cv2.COLOR_BGR2RGB)
target = {}
target3 = {'image0': 'image', 'image1': 'image', 'image2': 'image'}
transformed = albu.Compose(co_aug_transforms, p=1, additional_targets=target3)(image=frame1,
                                                                                         image0=frame2,
                                                                                         image1=flow)

frame1 = transformed['image']
frame2 = transformed['image0']
flow = transformed['image1']