Confusing Particles Areas Data

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Confusing Particles Areas Data

I O Ogunniyi
Dear Users:

Please I am having problem making sense out data generated with Analyse Particles.

I am trying to estimate surface porosity of refractory samples.I auto-threshold the 32bit image to contrast the surface pores and got it as a network of black patches against white background. I calibrated the surface in microns and used Analysed Particles for the areas - sample images attached with resulting data. The problem is that I got extremes of particles areas far larger than the largest possible pore structure. I am therefore confused what exactly constitute the particles being analysed.

Could someone please help me  make sense out of this, or please guide me aright on the right approach to this task.

Thanks a lot.

'Tunji

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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1301 11249.263
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1360 12227.459
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1369 12390.492
1370 12390.492
1371 12553.525
1372 12553.525
1373 12553.525
1374 12553.525
1375 12553.525
1376 12553.525
1377 12553.525
1378 12553.525
1379 12553.525
1380 12553.525
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1382 12716.558
1383 12716.558
1384 12716.558
1385 12716.558
1386 12716.558
1387 12716.558
1388 12716.558
1389 12716.558
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1391 13042.623
1392 13042.623
1393 13042.623
1394 13042.623
1395 13042.623
1396 13042.623
1397 13042.623
1398 13042.623
1399 13042.623
1400 13042.623
1401 13205.656
1402 13205.656
1403 13205.656
1404 13205.656
1405 13205.656
1406 13205.656
1407 13205.656
1408 13205.656
1409 13368.689
1410 13368.689
1411 13368.689
1412 13368.689
1413 13368.689
1414 13531.722
1415 13531.722
1416 13531.722
1417 13531.722
1418 13531.722
1419 13531.722
1420 13531.722
1421 13531.722
1422 13531.722
1423 13531.722
1424 13531.722
1425 13531.722
1426 13531.722
1427 13531.722
1428 13694.754
1429 13694.754
1430 13694.754
1431 13694.754
1432 13694.754
1433 13694.754
1434 13694.754
1435 13694.754
1436 13857.787
1437 13857.787
1438 13857.787
1439 13857.787
1440 13857.787
1441 13857.787
1442 13857.787
1443 13857.787
1444 13857.787
1445 14020.82
1446 14020.82
1447 14020.82
1448 14020.82
1449 14020.82
1450 14020.82
1451 14183.853
1452 14183.853
1453 14183.853
1454 14183.853
1455 14183.853
1456 14183.853
1457 14346.886
1458 14346.886
1459 14346.886
1460 14509.918
1461 14509.918
1462 14509.918
1463 14509.918
1464 14509.918
1465 14509.918
1466 14509.918
1467 14509.918
1468 14672.951
1469 14672.951
1470 14672.951
1471 14672.951
1472 14672.951
1473 14672.951
1474 14672.951
1475 14672.951
1476 14835.984
1477 14835.984
1478 14835.984
1479 14835.984
1480 14835.984
1481 14999.017
1482 14999.017
1483 14999.017
1484 14999.017
1485 14999.017
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1487 14999.017
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1491 14999.017
1492 14999.017
1493 14999.017
1494 14999.017
1495 14999.017
1496 15162.05
1497 15162.05
1498 15162.05
1499 15162.05
1500 15162.05
1501 15162.05
1502 15162.05
1503 15162.05
1504 15162.05
1505 15325.082
1506 15325.082
1507 15325.082
1508 15488.115
1509 15488.115
1510 15488.115
1511 15488.115
1512 15488.115
1513 15651.148
1514 15651.148
1515 15651.148
1516 15651.148
1517 15651.148
1518 15814.181
1519 15814.181
1520 15814.181
1521 15814.181
1522 15814.181
1523 15814.181
1524 15814.181
1525 15977.214
1526 15977.214
1527 15977.214
1528 15977.214
1529 15977.214
1530 15977.214
1531 15977.214
1532 15977.214
1533 16140.246
1534 16140.246
1535 16303.279
1536 16303.279
1537 16303.279
1538 16303.279
1539 16303.279
1540 16303.279
1541 16303.279
1542 16466.312
1543 16466.312
1544 16466.312
1545 16466.312
1546 16466.312
1547 16629.345
1548 16629.345
1549 16629.345
1550 16629.345
1551 16629.345
1552 16792.378
1553 16792.378
1554 16792.378
1555 16792.378
1556 16792.378
1557 16792.378
1558 16955.41
1559 16955.41
1560 16955.41
1561 16955.41
1562 16955.41
1563 16955.41
1564 16955.41
1565 17118.443
1566 17118.443
1567 17118.443
1568 17118.443
1569 17118.443
1570 17118.443
1571 17118.443
1572 17118.443
1573 17118.443
1574 17118.443
1575 17281.476
1576 17281.476
1577 17281.476
1578 17281.476
1579 17281.476
1580 17444.509
1581 17444.509
1582 17444.509
1583 17444.509
1584 17607.541
1585 17607.541
1586 17607.541
1587 17607.541
1588 17607.541
1589 17607.541
1590 17607.541
1591 17770.574
1592 17770.574
1593 17770.574
1594 17770.574
1595 17770.574
1596 17933.607
1597 17933.607
1598 17933.607
1599 18096.64
1600 18096.64
1601 18096.64
1602 18096.64
1603 18096.64
1604 18096.64
1605 18259.673
1606 18259.673
1607 18259.673
1608 18422.705
1609 18422.705
1610 18422.705
1611 18422.705
1612 18422.705
1613 18422.705
1614 18422.705
1615 18585.738
1616 18585.738
1617 18585.738
1618 18585.738
1619 18585.738
1620 18748.771
1621 18748.771
1622 18748.771
1623 18748.771
1624 18748.771
1625 18748.771
1626 18911.804
1627 18911.804
1628 18911.804
1629 18911.804
1630 18911.804
1631 19074.837
1632 19074.837
1633 19074.837
1634 19074.837
1635 19237.869
1636 19237.869
1637 19237.869
1638 19237.869
1639 19237.869
1640 19400.902
1641 19400.902
1642 19400.902
1643 19400.902
1644 19563.935
1645 19563.935
1646 19563.935
1647 19563.935
1648 19563.935
1649 19726.968
1650 19726.968
1651 19726.968
1652 19726.968
1653 19726.968
1654 19726.968
1655 19726.968
1656 19726.968
1657 19726.968
1658 19890.001
1659 19890.001
1660 19890.001
1661 20053.033
1662 20053.033
1663 20053.033
1664 20053.033
1665 20216.066
1666 20216.066
1667 20216.066
1668 20216.066
1669 20216.066
1670 20216.066
1671 20216.066
1672 20379.099
1673 20379.099
1674 20379.099
1675 20379.099
1676 20379.099
1677 20542.132
1678 20542.132
1679 20542.132
1680 20542.132
1681 20542.132
1682 20542.132
1683 20542.132
1684 20542.132
1685 20705.165
1686 20705.165
1687 20705.165
1688 20705.165
1689 20705.165
1690 20868.197
1691 20868.197
1692 20868.197
1693 21031.23
1694 21031.23
1695 21031.23
1696 21031.23
1697 21031.23
1698 21194.263
1699 21194.263
1700 21357.296
1701 21357.296
1702 21357.296
1703 21357.296
1704 21357.296
1705 21357.296
1706 21357.296
1707 21357.296
1708 21357.296
1709 21357.296
1710 21357.296
1711 21520.328
1712 21520.328
1713 21520.328
1714 21520.328
1715 21520.328
1716 21520.328
1717 21520.328
1718 21520.328
1719 21520.328
1720 21683.361
1721 21683.361
1722 21683.361
1723 21846.394
1724 21846.394
1725 21846.394
1726 21846.394
1727 22009.427
1728 22009.427
1729 22009.427
1730 22009.427
1731 22009.427
1732 22009.427
1733 22009.427
1734 22172.46
1735 22172.46
1736 22335.492
1737 22335.492
1738 22335.492
1739 22335.492
1740 22335.492
1741 22335.492
1742 22335.492
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1744 22498.525
1745 22498.525
1746 22498.525
1747 22661.558
1748 22661.558
1749 22661.558
1750 22824.591
1751 22824.591
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1753 22987.624
1754 22987.624
1755 23150.656
1756 23150.656
1757 23150.656
1758 23150.656
1759 23150.656
1760 23150.656
1761 23313.689
1762 23313.689
1763 23313.689
1764 23313.689
1765 23313.689
1766 23313.689
1767 23313.689
1768 23476.722
1769 23476.722
1770 23476.722
1771 23476.722
1772 23639.755
1773 23639.755
1774 23639.755
1775 23639.755
1776 23802.788
1777 23802.788
1778 23802.788
1779 23965.82
1780 23965.82
1781 24128.853
1782 24128.853
1783 24291.886
1784 24291.886
1785 24291.886
1786 24291.886
1787 24291.886
1788 24291.886
1789 24454.919
1790 24454.919
1791 24454.919
1792 24617.952
1793 24617.952
1794 24780.984
1795 24780.984
1796 24780.984
1797 24780.984
1798 24944.017
1799 24944.017
1800 24944.017
1801 25107.05
1802 25107.05
1803 25107.05
1804 25270.083
1805 25270.083
1806 25270.083
1807 25270.083
1808 25270.083
1809 25270.083
1810 25433.115
1811 25433.115
1812 25433.115
1813 25596.148
1814 25596.148
1815 25596.148
1816 25596.148
1817 25596.148
1818 25759.181
1819 25759.181
1820 25759.181
1821 26085.247
1822 26085.247
1823 26085.247
1824 26085.247
1825 26248.279
1826 26248.279
1827 26411.312
1828 26411.312
1829 26574.345
1830 26574.345
1831 26574.345
1832 26737.378
1833 26737.378
1834 26737.378
1835 26737.378
1836 26737.378
1837 26900.411
1838 26900.411
1839 26900.411
1840 26900.411
1841 26900.411
1842 27063.443
1843 27063.443
1844 27063.443
1845 27226.476
1846 27226.476
1847 27226.476
1848 27226.476
1849 27226.476
1850 27226.476
1851 27389.509
1852 27389.509
1853 27389.509
1854 27715.575
1855 27715.575
1856 27715.575
1857 27715.575
1858 27878.607
1859 27878.607
1860 27878.607
1861 27878.607
1862 27878.607
1863 28041.64
1864 28041.64
1865 28041.64
1866 28041.64
1867 28204.673
1868 28204.673
1869 28204.673
1870 28204.673
1871 28204.673
1872 28204.673
1873 28367.706
1874 28367.706
1875 28367.706
1876 28367.706
1877 28367.706
1878 28367.706
1879 28530.739
1880 28530.739
1881 28530.739
1882 28530.739
1883 28693.771
1884 28856.804
1885 28856.804
1886 28856.804
1887 29019.837
1888 29019.837
1889 29182.87
1890 29182.87
1891 29182.87
1892 29345.902
1893 29508.935
1894 29508.935
1895 29508.935
1896 29671.968
1897 29671.968
1898 29671.968
1899 29671.968
1900 29671.968
1901 29835.001
1902 29835.001
1903 29835.001
1904 29998.034
1905 29998.034
1906 29998.034
1907 30161.066
1908 30161.066
1909 30324.099
1910 30324.099
1911 30324.099
1912 30324.099
1913 30487.132
1914 30487.132
1915 30650.165
1916 30650.165
1917 30813.198
1918 30813.198
1919 30976.23
1920 30976.23
1921 30976.23
1922 30976.23
1923 30976.23
1924 31139.263
1925 31139.263
1926 31302.296
1927 31465.329
1928 31628.362
1929 31628.362
1930 31628.362
1931 31791.394
1932 31791.394
1933 31954.427
1934 31954.427
1935 31954.427
1936 31954.427
1937 31954.427
1938 32117.46
1939 32117.46
1940 32280.493
1941 32280.493
1942 32280.493
1943 32280.493
1944 32280.493
1945 32443.526
1946 32606.558
1947 32606.558
1948 32606.558
1949 32606.558
1950 32606.558
1951 32769.591
1952 32932.624
1953 32932.624
1954 33095.657
1955 33095.657
1956 33258.689
1957 33258.689
1958 33258.689
1959 33421.722
1960 33421.722
1961 33421.722
1962 33421.722
1963 33421.722
1964 33421.722
1965 33584.755
1966 33747.788
1967 33910.821
1968 33910.821
1969 34073.853
1970 34073.853
1971 34073.853
1972 34073.853
1973 34236.886
1974 34236.886
1975 34562.952
1976 34725.985
1977 34725.985
1978 34889.017
1979 34889.017
1980 34889.017
1981 34889.017
1982 35052.05
1983 35052.05
1984 35052.05
1985 35215.083
1986 35215.083
1987 35215.083
1988 35215.083
1989 35215.083
1990 35215.083
1991 35215.083
1992 35378.116
1993 35378.116
1994 35378.116
1995 35541.149
1996 35541.149
1997 35704.181
1998 35704.181
1999 35704.181
2000 35704.181
2001 35867.214
2002 35867.214
2003 35867.214
2004 36030.247
2005 36030.247
2006 36030.247
2007 36356.313
2008 36356.313
2009 36519.345
2010 36519.345
2011 36519.345
2012 36519.345
2013 36519.345
2014 36682.378
2015 36682.378
2016 36682.378
2017 36682.378
2018 36845.411
2019 36845.411
2020 36845.411
2021 37008.444
2022 37008.444
2023 37008.444
2024 37171.476
2025 37497.542
2026 37497.542
2027 37497.542
2028 37660.575
2029 37660.575
2030 37823.608
2031 37823.608
2032 37823.608
2033 37986.64
2034 37986.64
2035 37986.64
2036 37986.64
2037 38149.673
2038 38149.673
2039 38312.706
2040 38312.706
2041 38475.739
2042 38475.739
2043 38475.739
2044 38475.739
2045 38638.772
2046 38638.772
2047 38638.772
2048 38638.772
2049 38638.772
2050 38638.772
2051 39127.87
2052 39127.87
2053 39127.87
2054 39290.903
2055 39290.903
2056 39290.903
2057 39290.903
2058 39453.936
2059 39453.936
2060 39453.936
2061 39616.968
2062 39616.968
2063 39616.968
2064 39780.001
2065 39780.001
2066 39780.001
2067 39780.001
2068 39943.034
2069 39943.034
2070 39943.034
2071 40106.067
2072 40106.067
2073 40269.1
2074 40269.1
2075 40269.1
2076 40269.1
2077 40595.165
2078 40595.165
2079 40595.165
2080 40595.165
2081 40595.165
2082 40758.198
2083 40758.198
2084 40921.231
2085 41247.296
2086 41247.296
2087 41247.296
2088 41410.329
2089 41736.395
2090 41899.427
2091 42062.46
2092 42062.46
2093 42062.46
2094 42225.493
2095 42225.493
2096 42388.526
2097 42388.526
2098 42388.526
2099 42551.559
2100 42551.559
2101 42551.559
2102 42551.559
2103 42551.559
2104 42714.591
2105 42714.591
2106 42714.591
2107 42877.624
2108 42877.624
2109 42877.624
2110 42877.624
2111 43203.69
2112 43203.69
2113 43366.723
2114 43366.723
2115 43529.755
2116 43692.788
2117 43855.821
2118 44018.854
2119 44018.854
2120 44181.887
2121 44181.887
2122 44344.919
2123 44507.952
2124 44507.952
2125 44670.985
2126 44834.018
2127 44834.018
2128 44997.05
2129 45160.083
2130 45323.116
2131 45486.149
2132 45649.182
2133 45649.182
2134 45812.214
2135 45975.247
2136 46301.313
2137 46464.346
2138 46464.346
2139 46627.378
2140 46627.378
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Re: Confusing Particles Areas Data

Cameron Nowell
Hi 'Tunji,

When you use the analyse particles module you can change the show value to show the masks or outlines of the objects it is measuring. That will help you figure out what could be going wrong.

You could also add a cut off to the size being measured to exclude erroneous large bits


Cheers

Cam



Cameron J. Nowell
Scientific Imaging and Analysis Specialist
Centre for Dynamic Imaging
The Walter and Eliza Hall Institute of Medical Research
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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Iyiola Olatunji Otunniyi
Sent: Friday, 24 May 2013 5:44 AM
To: [hidden email]
Subject: Confusing Particles Areas Data

Dear Users:

Please I am having problem making sense out data generated with Analyse Particles.

I am trying to estimate surface porosity of refractory samples.I auto-threshold the 32bit image to contrast the surface pores and got it as a network of black patches against white background. I calibrated the surface in microns and used Analysed Particles for the areas - sample images attached with resulting data. The problem is that I got extremes of particles areas far larger than the largest possible pore structure. I am therefore confused what exactly constitute the particles being analysed.

Could someone please help me  make sense out of this, or please guide me aright on the right approach to this task.

Thanks a lot.

'Tunji

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Re: Confusing Particles Areas Data

Michael Schmid
In reply to this post by I O Ogunniyi
Hi Tunji,

looking at your list of results, it seems that you have had a pixel size of 163 um^2 (or whatever units you use). On such an image, thresholding always gives you many very small particles with 1, 2, 3, .. pixels.
For some reason, the list is sorted by area ('Analyze Particles' does not sort by area).

When I try with the image (h) supplied by you and applying a reasonable threshold (0-70 after conversion of your image to grayscale), the largest size I get is about 5 million um^2. This is at the border, near the bottom at the 7 o'clock position. If you slightly increase the upper the threshold, it will merge with a void at its left and then with the 2 million um^2 void at a 5 o'clock position.

There is also a large void near the 4 o'clock position, but it is difficult for me to say how large it actually is - it may be connected via a channel with the void near 2 o'clock, the it is much larger. Then it would be some 20 million um^2, roughly the maximum size in your list.

If you want to see the largest voids ('particles') from your run of 'Analyze particles', select a suitable size range, e.g. 1000000-Infinity, and Show:Masks.

Then you can use the Wand tool to mark each of the particles (double-click it and set to '8-connected' and 'Measure' to see its size in the Results Window. The Wand also works in the original thresholded image, but there it is more difficult to see the borders of the particles.

This will show you where the large particles are situated.

If you are unhappy with the current results, you will probably need better illumination (very grazing angle, from different sides or from a ring all around).

Michael
________________________________________________________________
On May 23, 2013, at 21:44, Iyiola Olatunji Otunniyi wrote:

> Dear Users:
>
> Please I am having problem making sense out data generated with Analyse Particles.
>
> I am trying to estimate surface porosity of refractory samples.I auto-threshold the 32bit image to contrast the surface pores and got it as a network of black patches against white background. I calibrated the surface in microns and used Analysed Particles for the areas - sample images attached with resulting data. The problem is that I got extremes of particles areas far larger than the largest possible pore structure. I am therefore confused what exactly constitute the particles being analysed.
>
> Could someone please help me  make sense out of this, or please guide me aright on the right approach to this task.
>
> Thanks a lot.
>
> 'Tunji

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