Images are composed of pixels (pix - picture, el - element).
In a grayscale image the pixel contains the intensity. Depending on the image format this may range from 0-1, 0-255, or be any floating point number.
In a color image a pixel is (usually) a triple (red,green,blue) of color values where each color intensity ranges from 0-255 (24-bit color).
It is very common for RGB color values to be represented in hexadecimal (e.g., HTML).
Hexadecimal number are usually indicated with a 0x
or #
prefix.
In hexadecimal, each digit can take one of 16 values (as opposed to 10). This means that each color can be represented with two digits (16*16 = 256)
Hex | Dec |
---|---|
A | 10 |
B | 11 |
C | 12 |
D | 13 |
E | 14 |
F | 15 |
31 254
<div style="color: #ff00ff">Hello</div>
The Python Imaging Library provides the ability to read, write an manipulate images in all the common formats. Some key modules:
Despite being a popular package, PIL development stopped in 2011 with no new releases since 2009.
Pillow is a fork of PIL that is fully backwards compatible and updated (and is what you are actually using rather than the original PIL).
Actin HSP27 DAPI
PIL refers to the different color channels as bands.
('R', 'G', 'B')
You can split a color image into it's separate bands.
We can convert to grayscale ('L' - luminance)
(640, 480)
(159, 3, 18)
To get/set pixels directly, first load the pixel map of an image.
Can convert to numpy
array - first dimension (rows) will be y-axis
(480, 640, 3)
array([159, 3, 18], dtype=uint8)
Can get all the pixels in a flat list
[(243, 3, 28), (238, 3, 27), (242, 3, 26), (239, 3, 27), (226, 3, 27), (220, 3, 26), (195, 3, 27), (179, 3, 26), (171, 3, 27), (163, 4, 28), (163, 3, 27), (148, 3, 28), (145, 4, 27), (146, 3, 27), (137, 4, 27), (136, 4, 27), (136, 3, 28), (124, 4, 28), (125, 4, 28), (121, 3, 27), (116, 4, 28), (113, 4, 26), (107, 3, 28), (107, 4, 27), (103, 3, 29), (96, 3, 28), (93, 3, 30), (95, 3, 27), (87, 3, 28), (94, 3, 28), (91, 3, 27), (94, 3, 28), (87, 3, 27), (93, 3, 28), (82, 3, 27), (79, 3, 28), (78, 4, 27), (84, 4, 28), (79, 4, 29), (85, 4, 28), (82, 4, 29), (83, 3, 29), (81, 3, 30), (70, 4, 30), (79, 4, 28), (78, 4, 29), (77, 4, 28), (81, 4, 29), (80, 4, 30), (72, 3, 30), (76, 4, 30), (77, 4, 30), (84, 4, 29), (84, 4, 31), (80, 4, 30), (87, 4, 33), (88, 4, 31), (89, 4, 34), (89, 4, 32), (96, 4, 33), (89, 4, 32), (91, 4, 33), (92, 4, 32), (93, 4, 31), (96, 4, 31), (96, 4, 30), (103, 4, 31), (103, 4, 31), (93, 4, 31), (106, 4, 30), (100, 4, 31), (105, 4, 31), (108, 4, 31), (106, 4, 32), (110, 4, 32), (101, 4, 31), (105, 3, 32), (102, 4, 32), (107, 4, 33), (114, 3, 34), (111, 4, 35), (106, 4, 36), (104, 4, 35), (106, 4, 35), (112, 4, 37), (120, 4, 40), (107, 4, 39), (108, 4, 41), (110, 4, 43), (107, 4, 46), (102, 3, 47), (108, 4, 47), (109, 4, 48), (106, 3, 51), (106, 4, 49), (103, 4, 53), (99, 4, 53), (102, 4, 55), (99, 4, 58), (109, 4, 58), (104, 4, 60), (97, 4, 59), (101, 5, 59), (91, 4, 60), (96, 3, 58), (92, 4, 60), (97, 4, 62), (96, 4, 65), (92, 4, 66), (95, 4, 69), (92, 4, 70), (91, 4, 69), (91, 3, 68), (93, 3, 66), (96, 4, 66), (92, 3, 65), (98, 3, 64), (86, 3, 62), (88, 4, 64), (95, 3, 64), (97, 3, 63), (81, 3, 64), (82, 4, 64), (88, 3, 63), (84, 3, 65), (75, 3, 66), (79, 4, 69), (84, 3, 68), (86, 3, 68), (83, 3, 66), (84, 3, 65), (81, 3, 64), (81, 3, 65), (87, 3, 66), (78, 3, 64), (86, 3, 64), (83, 3, 65), (82, 3, 62), (82, 3, 64), (83, 3, 64), (90, 3, 65), (82, 3, 64), (88, 3, 62), (83, 3, 64), (83, 4, 64), (91, 3, 62), (87, 3, 58), (81, 3, 58), (87, 3, 57), (80, 3, 56), (88, 3, 52), (84, 3, 49), (86, 3, 47), (86, 3, 48), (81, 3, 44), (81, 3, 41), (80, 2, 40), (88, 3, 39), (87, 3, 38), (82, 3, 38), (89, 2, 36), (83, 3, 37), (83, 3, 35), (88, 2, 34), (84, 3, 34), (83, 3, 33), (83, 3, 33), (84, 2, 33), (89, 3, 33), (85, 3, 32), (84, 3, 31), (88, 3, 31), (86, 3, 31), (89, 3, 32), (88, 2, 31), (90, 3, 31), (91, 3, 31), (88, 3, 31), (90, 2, 30), (96, 3, 31), (96, 2, 32), (103, 3, 30), (106, 3, 28), (106, 2, 28), (113, 2, 29), (110, 2, 29), (104, 2, 30), (110, 2, 29), (101, 2, 29), (103, 2, 29), (107, 2, 28), (107, 3, 29), (108, 3, 28), (102, 2, 28), (107, 2, 28), (104, 2, 28), (105, 2, 29), (114, 2, 29), (105, 3, 29), (109, 2, 29), (109, 2, 29), (111, 2, 30), (110, 2, 29), (106, 2, 29), (119, 2, 31), (117, 2, 30), (112, 2, 30), (114, 2, 30), (114, 2, 28), (124, 2, 30), (124, 2, 30), (119, 2, 30), (124, 2, 30), (117, 2, 32), (118, 2, 29), (126, 2, 30), (124, 2, 28), (128, 2, 31), (128, 3, 30), (130, 2, 31), (135, 2, 30), (124, 2, 30), (134, 2, 30), (132, 2, 30), (138, 2, 31), (146, 2, 31), (149, 2, 31), (141, 2, 32), (139, 2, 30), (148, 2, 32), (146, 2, 32), (151, 2, 32), (151, 2, 32), (154, 2, 34), (167, 2, 35), (158, 2, 33), (162, 2, 34), (169, 2, 35), (175, 2, 34), (179, 2, 36), (186, 2, 36), (177, 2, 36), (186, 1, 36), (186, 2, 37), (196, 1, 38), (192, 1, 38), (194, 2, 39), (195, 1, 38), (204, 2, 39), (210, 2, 40), (205, 1, 38), (205, 2, 40), (215, 2, 39), (200, 1, 42), (205, 1, 41), (212, 1, 42), (221, 1, 43), (219, 1, 42), (216, 1, 45), (215, 1, 45), (203, 1, 47), (213, 2, 46), (191, 1, 47), (206, 2, 46), (207, 2, 46), (191, 1, 48), (180, 1, 50), (162, 1, 49), (165, 1, 52), (149, 1, 52), (154, 1, 54), (142, 1, 54), (143, 1, 55), (139, 1, 56), (133, 1, 58), (135, 1, 59), (136, 1, 58), (131, 1, 60), (136, 1, 61), (136, 1, 60), (136, 2, 62), (141, 1, 62), (135, 1, 62), (137, 2, 66), (132, 2, 68), (140, 1, 68), (146, 1, 69), (153, 2, 71), (138, 1, 73), (134, 1, 72), (139, 1, 74), (138, 1, 76), (140, 1, 76), (127, 2, 80), (136, 1, 82), (139, 1, 80), (129, 1, 83), (136, 1, 83), (137, 1, 83), (133, 2, 82), (129, 1, 86), (139, 1, 84), (131, 1, 83), (138, 1, 85), (139, 2, 83), (140, 1, 84), (150, 1, 87), (146, 1, 87), (147, 1, 85), (142, 1, 86), (144, 1, 85), (146, 1, 84), (151, 1, 85), (151, 1, 87), (146, 1, 85), (141, 1, 85), (141, 2, 84), (156, 1, 84), (157, 1, 87), (153, 1, 88), (153, 1, 92), (151, 1, 96), (147, 1, 98), (151, 1, 96), (154, 1, 91), (150, 1, 87), (158, 1, 83), (151, 1, 80), (154, 1, 80), (166, 1, 78), (174, 1, 76), (175, 1, 72), (179, 1, 70), (179, 1, 68), (183, 1, 67), (182, 2, 66), (180, 1, 63), (183, 1, 62), (180, 1, 59), (184, 1, 58), (178, 1, 55), (187, 2, 55), (187, 1, 52), (176, 1, 52), (156, 1, 50), (147, 1, 51), (155, 1, 50), (138, 1, 49), (139, 2, 49), (132, 1, 47), (126, 1, 46), (116, 1, 46), (125, 1, 44), (123, 1, 45), (116, 1, 45), (118, 2, 43), (106, 1, 42), (111, 1, 43), (112, 2, 42), (99, 1, 42), (99, 1, 41), (100, 1, 39), (100, 2, 38), (99, 1, 38), (98, 1, 37), (96, 1, 36), (100, 1, 34), (98, 1, 35), (90, 2, 34), (92, 1, 33), (95, 1, 33), (95, 1, 33), (97, 1, 31), (89, 1, 30), (89, 1, 31), (102, 1, 30), (97, 2, 29), (94, 1, 29), (90, 1, 27), (91, 1, 27), (90, 1, 27), (88, 1, 25), (94, 1, 26), (96, 1, 25), (90, 1, 26), (98, 1, 25), (98, 1, 24), (103, 1, 22), (108, 1, 22), (112, 1, 22), (123, 1, 21), (125, 1, 21), (107, 1, 21), (96, 1, 20), (92, 1, 21), (83, 2, 19), (83, 1, 19), (80, 1, 20), (75, 1, 19), (75, 1, 19), (72, 1, 18), (73, 1, 19), (68, 1, 18), (70, 1, 18), (64, 1, 18), (66, 1, 18), (65, 1, 17), (57, 1, 17), (55, 1, 16), (63, 1, 17), (58, 1, 17), (58, 1, 17), (61, 1, 16), (58, 1, 16), (56, 1, 16), (64, 1, 17), (68, 1, 17), (64, 1, 16), (67, 1, 16), (58, 1, 16), (64, 1, 15), (65, 1, 15), (56, 1, 15), (61, 1, 16), (61, 1, 16), (61, 1, 15), (56, 1, 16), (55, 1, 15), (48, 1, 16), (46, 1, 15), (45, 1, 15), (49, 1, 15), (42, 1, 15), (42, 1, 15), (47, 1, 14), (39, 1, 14), (40, 1, 14), (44, 1, 14), (42, 1, 15), (43, 1, 15), (45, 1, 14), (44, 1, 14), (52, 1, 15), (40, 1, 14), (40, 1, 14), (33, 1, 14), (35, 1, 14), (37, 1, 14), (40, 1, 16), (42, 1, 15), (45, 1, 14), (44, 1, 14), (49, 1, 15), (55, 1, 15), (53, 1, 15), (49, 1, 15), (49, 1, 14), (56, 1, 15), (49, 1, 15), (49, 1, 16), (52, 1, 15), (58, 1, 15), (48, 1, 14), (56, 1, 15), (52, 2, 15), (56, 1, 15), (59, 2, 14), (59, 1, 15), (59, 1, 15), (54, 1, 14), (48, 1, 14), (44, 1, 14), (47, 1, 14), (48, 1, 14), (47, 1, 13), (42, 1, 14), (41, 1, 13), (42, 1, 12), (43, 1, 13), (45, 1, 13), (41, 1, 13), (53, 1, 13), (52, 1, 13), (49, 1, 13), (45, 1, 13), (35, 1, 13), (28, 1, 12), (32, 1, 12), (30, 1, 12), (30, 1, 12), (32, 1, 12), (27, 1, 12), (23, 1, 12), (25, 1, 12), (23, 1, 12), (23, 1, 12), (23, 1, 12), (21, 1, 12), (25, 1, 12), (21, 1, 11), (19, 1, 12), (24, 1, 12), (20, 1, 12), (21, 1, 12), (20, 1, 12), (19, 1, 12), (21, 1, 12), (19, 1, 11), (17, 1, 11), (21, 1, 12), (14, 1, 12), (15, 1, 12), (17, 1, 12), (14, 1, 12), (19, 1, 12), (12, 1, 12), (16, 1, 12), (16, 1, 12), (15, 1, 12), (11, 1, 11), (14, 1, 12), (12, 1, 12), (15, 1, 11), (11, 2, 11), (11, 1, 12), (12, 1, 11), (11, 1, 12), (12, 1, 12), (12, 1, 12), (12, 1, 12), (13, 1, 12), (15, 1, 11), (8, 2, 12), (9, 1, 11), (10, 1, 12), (10, 1, 12), (7, 1, 11), (12, 1, 12), (12, 1, 12), (10, 1, 12), (11, 1, 11), (11, 1, 11), (10, 1, 12), (10, 1, 11), (12, 1, 11), (9, 1, 11), (11, 1, 12), (12, 1, 12), (9, 1, 11), (11, 1, 12), (10, 1, 12), (13, 1, 12), (12, 1, 11), (13, 1, 11), (13, 1, 11), (14, 1, 11), (11, 1, 11), (12, 1, 10), (16, 1, 11), (14, 1, 12), (16, 1, 12), (18, 1, 11), (18, 1, 11), (19, 2, 11), (25, 1, 11), (26, 1, 12), (22, 1, 12), (29, 1, 11), (34, 2, 12), (38, 2, 11), (38, 1, 11), (50, 1, 11), (55, 2, 11), (62, 2, 11), (65, 2, 11), (78, 3, 12), (84, 2, 11), (90, 2, 11), (77, 2, 11), (66, 2, 11), (56, 2, 12), (50, 2, 11), (42, 2, 11), (39, 2, 12), (41, 2, 12), (38, 3, 11), (41, 2, 11), (32, 2, 12), (38, 3, 10), (39, 2, 11), (37, 2, 11), (35, 2, 11), (34, 3, 12), (37, 3, 12), (33, 3, 12), (34, 3, 12), (37, 2, 12), (41, 4, 12), (32, 3, 12), (37, 3, 12), (37, 3, 12), (28, 4, 12), (25, 4, 12), (23, 4, 12), (29, 4, 12), (27, 4, 11), (32, 4, 12), (30, 5, 11), (25, 5, 12), (26, 5, 12), (22, 6, 12), (27, 5, 12), (24, 5, 13), (24, 5, 12), (24, 5, 12), (19, 6, 14), (24, 6, 13), (20, 6, 13), (18, 6, 13), (24, 7, 13), (20, 7, 14), (22, 7, 13), (17, 6, 13), (16, 7, 13), (19, 6, 14), (23, 7, 14), (18, 8, 14), (27, 8, 14), (21, 7, 13), (20, 7, 14), (22, 7, 14), (23, 7, 14), (21, 7, 14), (22, 6, 14), (22, 6, 14), (18, 6, 14), (18, 6, 15), (20, 6, 14), (19, 6, 14), (18, 6, 14), (248, 3, 26), (249, 3, 27), (246, 3, 27), (237, 3, 27), (221, 3, 27), (198, 3, 26), (180, 4, 26), (167, 4, 27), (158, 4, 28), (160, 4, 26), (151, 3, 27), (147, 3, 28), (147, 3, 28), (136, 4, 28), (140, 4, 28), (141, 3, 28), (136, 3, 28), (127, 3, 28), (122, 3, 29), (120, 3, 27), (115, 3, 29), (114, 3, 27), (112, 3, 29), (107, 3, 28), (102, 3, 29), (92, 4, 28), (92, 4, 27), (94, 3, 28), (91, 3, 28), (98, 4, 28), (85, 3, 27), (88, 3, 29), (85, 3, 27), (87, 4, 28), (92, 3, 26), (84, 4, 27), (92, 4, 27), (75, 3, 29), (81, 4, 29), (84, 4, 30), (78, 4, 28), (78, 4, 30), (77, 4, 30), (85, 4, 29), (75, 4, 30), (77, 4, 30), (79, 4, 29), (75, 4, 29), (74, 4, 30), (86, 4, 30), (76, 4, 29), (83, 4, 30), (83, 4, 30), (83, 4, 30), (83, 5, 31), (83, 4, 33), (90, 4, 33), (89, 4, 35), (82, 4, 34), (91, 4, 34), (90, 4, 33), (97, 4, 31), (93, 4, 33), (92, 5, 30), (94, 4, 31), (92, 4, 31), (102, 4, 31), (100, 5, 31), (99, 4, 29), (104, 4, 31), (106, 4, 32), (99, 4, 32), (110, 4, 31), (105, 4, 31), (109, 4, 32), (112, 4, 32), (105, 4, 32), (117, 4, 33), (111, 4, 33), (107, 4, 33), (114, 5, 35), (119, 4, 36), (106, 5, 37), (108, 5, 38), (118, 4, 38), (111, 4, 39), (112, 4, 42), (108, 5, 42), (110, 4, 44), (105, 4, 46), (106, 4, 47), (107, 4, 47), (105, 4, 48), (107, 4, 51), (103, 4, 51), (101, 4, 52), (108, 4, 53), (103, 4, 56), (105, 4, 60), (100, 4, 62), (98, 4, 62), (97, 4, 64), (98, 4, 63), (95, 4, 62), (100, 4, 60), (96, 4, 61), (91, 4, 64), (94, 4, 68), (94, 4, 71), (97, 4, 72), (89, 4, 74), (91, 4, 76), (89, 4, 73), (91, 3, 69), (81, 3, 69), (90, 3, 70), (89, 4, 67), (91, 4, 68), (91, 4, 67), (81, 4, 66), (80, 3, 65), (87, 4, 66), (87, 3, 66), (88, 3, 65), (86, 4, 63), (86, 3, 67), (85, 3, 69), (82, 3, 70), (84, 4, 71), (88, 4, 69), (75, 3, 67), (83, 3, 65), (80, 4, 65), (77, 3, 65), (87, 3, 64), (87, 3, 65), (87, 4, 64), (82, 3, 64), (81, 3, 64), (82, 3, 65), (83, 3, 67), (83, 3, 66), (92, 3, 67), (82, 3, 68), (84, 3, 62), (79, 3, 61), (88, 2, 61), (87, 3, 60), (83, 3, 57), (86, 3, 56), (89, 3, 53), (86, 3, 52), (83, 3, 51), (83, 3, 49), (79, 3, 44), (92, 3, 44), (87, 3, 40), (81, 3, 37), (88, 3, 38), (83, 3, 37), (85, 3, 36), (90, 4, 36), (88, 3, 36), (87, 3, 34), (82, 3, 35), (90, 2, 35), (89, 2, 33), (81, 3, 32), (81, 3, 33), (90, 3, 32), (89, 2, 32), (90, 2, 32), (88, 2, 33), (86, 3, 32), (93, 3, 32), (88, 2, 30), (89, 3, 31), (96, 3, 30), (91, 3, 30), (95, 3, 30), (103, 2, 30), (102, 2, 29), (109, 2, 30), (109, 3, 28), (109, 3, 28), (115, 3, 29), (112, 3, 27), (107, 3, 29), (106, 2, 29), (101, 3, 28), (109, 2, 29), (103, 3, 28), (100, 2, 28), (113, 2, 29), (111, 2, 28), (104, 2, 29), (115, 2, 29), (103, 2, 29), (107, 2, 29), (111, 2, 29), (108, 2, 30), (113, 2, 29), (115, 2, 30), (118, 2, 30), (115, 2, 30), (113, 2, 30), (122, 2, 31), (120, 2, 30), (113, 2, 30), (122, 2, 30), (123, 2, 32), (123, 2, 29), (124, 2, 29), (125, 2, 30), (121, 2, 28), (123, 2, 30), (125, 2, 29), (128, 2, 30), (137, 2, 30), (130, 2, 30), (130, 3, 29), (127, 2, 31), (129, 2, 31), (137, 2, 30), (143, 2, 30), (141, 2, 31), (138, 2, 31), (140, 2, 31), (140, 2, 31), (147, 2, 31), (149, 2, 33), (149, 2, 32), (153, 2, 32), (153, 2, 34), (159, 2, 33), (160, 2, 34), (170, 2, 35), (164, 2, 34), (181, 2, 35), (179, 2, 34), (177, 1, 35), (185, 2, 36), (184, 2, 37), (186, 2, 36), (195, 2, 36), (198, 2, 37), (198, 1, 37), (200, 2, 37), (204, 1, 39), (210, 1, 39), (210, 2, 40), (213, 1, 39), (200, 2, 41), (208, 2, 44), (220, 2, 42), (224, 2, 43), (212, 2, 44), (205, 1, 43), (211, 2, 43), (210, 2, 44), (209, 1, 45), (212, 1, 45), (214, 1, 47), (216, 1, 46), (206, 1, 46), (204, 2, 47), (192, 2, 49), (183, 2, 48), (174, 1, 51), (154, 1, 50), (156, 2, 54), (147, 1, 53), (143, 1, 52), (139, 1, 55), (139, 1, 56), (145, 1, 56), (135, 1, 58), (150, 1, 58), (136, 1, 57), (134, 2, 60), (141, 2, 62), (143, 1, 62), (143, 2, 64), (145, 1, 67), (145, 1, 66), (149, 1, 68), (149, 2, 66), (148, 1, 69), (141, 1, 69), (135, 1, 69), (139, 1, 73), (138, 1, 73), (143, 1, 74), (136, 2, 78), (150, 2, 76), (145, 1, 80), (137, 1, 79), (145, 1, 82), (135, 1, 80), (136, 1, 82), (139, 2, 83), (143, 1, 83), (144, 1, 80), (140, 2, 81), (151, 2, 84), (146, 1, 81), (147, 1, 82), (148, 1, 84), (154, 1, 82), (144, 1, 82), (152, 1, 83), (150, 2, 83), (154, 2, 83), (158, 1, 83), (158, 1, 82), (153, 1, 83), (152, 2, 85), (163, 1, 87), (160, 1, 87), (159, 1, 89), (162, 1, 90), (156, 1, 94), (158, 1, 96), (158, 1, 92), (166, 1, 88), (165, 1, 84), (168, 1, 79), (160, 1, 77), (168, 1, 78), (161, 1, 75), (176, 1, 74), (160, 1, 70), (177, 1, 67), (170, 1, 65), (176, 1, 63), (184, 1, 62), (172, 1, 60), (187, 1, 60), (189, 1, 59), (181, 1, 56), (187, 1, 54), (190, 1, 52), (184, 1, 51), (166, 1, 52), (161, 1, 53), (147, 1, 50), (138, 1, 48), (140, 1, 48), (134, 1, 48), (127, 1, 48), (129, 1, 48), (118, 1, 46), (129, 1, 43), (121, 1, 43), (107, 1, 42), (109, 1, 42), (110, 1, 42), (102, 1, 43), (103, 1, 40), (103, 1, 40), ...]
192
192
[(6, 192)]
[6, 14, 62, 172, 316, 517, 772, 1021, 1206, 1361, 1636, 2009, 2383, 2726, 3149, 3529, 3948, 4202, 4524, 4574]
(0.0, 24000.0)
Equalization attempts to normalizes the image histogram to create a uniform distribution of grayscale values. This makes it easier to see differences, but distorts the meaning of the intensities (the transformation is non-linear).
[<matplotlib.lines.Line2D at 0x1ff321ca880>]
Maximize (normalize) image contrast. This function calculates a histogram of the input image, removes a cutoff percent of the lightest and darkest pixels from the histogram, and remaps the image so that the darkest remaining pixel becomes black (0), and the lightest becomes white (255).
The point
function can be used to apply a function to every pixel in the image and return the transformed image. This makes it easy to threshold images into a mask.
Looking at the thresholded image, any thoughts on how to count the number of cells?
Sums for R: 20590309, G: 2241565, B: 8077411
Sums for R: 21396630, G: 4120230, B: 16723255