Measure surface in Avizo - Large data

Previously we measured surface in Avizo generated from a small label dataset. We created and saved each surface patch using “Surface View” module, and measured them separately using the “Surface Area Volume” module.

For large data, here I am talking about a surface generated from 1.44GB label dataset, the generated surface is of size 7GB. When I try to use “Surface View” to visualize the surface, Avizo crashes. So in this example we will avoid using surface view, instead measure the surface directly with “Surface Area Volume” module.

Step 1: clean the labels

Original data has some un-wanted label values. So use “Arithemtic” to clean up first. The expression is:

(A==1) + 2*(A==2) + 3*(A==3) + 4*(A==5) + 3*(A==4) + 3*(A>=6)

What this expression does is:

  1. Keep the label 0 (void), 1(clay), 2(feldspar), 3(quartz)
  2. Change the label 5(calcite) to 4(calcite)
  3. Merge labels 4, 6, 7, 8 to 3(quartz)

The result is a new file with data values:

0 (void), 1(clay), 2(feldspar), 3(quartz) and 4(calcite)

We save this data as label0-4.am in Avizo

Step 2: Generate surface

  1. Open label0-4.am, convert to 8-bit label, then open segmentation editor

  2. Chech the labels, rename them from “materials000x” to correct names – clay, feldspar, quartz, and calcite. Rename “Exterior” to “void”.

    _images/LTG-segmentation-editor.png

  3. Generate surface for the label data. Set “Smoothing type” port to “None”, uncheck “Add Border” in “Options” port.

Note: Don’t connect “surface view” module to created surface data.

Step 3: Measure Surface

  1. Connect “Measure surface area volume” module to the surf data, set Mode to “Patch”. show in spreadsheet

    _images/LTG-surface-statistics.png

  2. The Avizo network:

    _images/LTG-measure-network.png

Measurement Results:

  1. Total surface area of a phase is the sum of the surfac area connecting to other phases. For example, clay surface area = (clay/void + clay/feldspar + clay/quartz) surface area
  2. Total solid (clay + feldspar + quartz + calcite) surface area = void surface area
  3. void surface area = total solid surface area << sum of all phase surface area

statistics for data AGU_LTG

statistics for data AGU_LTG (1146 x 1173 x 1070)
phase void clay feldspar quartz calcite
void
28232436 71064 1302724 31
clay 28232436
116409 35138104
feldspar 71064 116409
678230
quartz 1302724 35138104 678230
718006
calcite 31
718006
sum 29606255 63486949 865703 37837064 718037

statistics for data AGU_LTG_EroadedClay_DilatedQuartz

statistics for data EroadedClay_DilatedQuartz (1146 x 1173 x 1070)
phase void clay altered feldspar quartz calcite
void
22917290 496509 7876340 25
clay 22917290
52881 28361572
altered feldspar 496509 52881
766432
quartz 7876340 28361572 766432
718012
calcite 25
718012
sum 31290164 51331743 1315822 37722356 718037

statistics for data AGU_SD

statistics for data AGU_SD (310 x 310 x 283)
phase void clay quartz calcite
void
942069 681007 5479
clay 942069
1207903 6574
quartz 681007 1207903
40309
calcite 5479 6574 40309
sum 1628555 2156546 1929219 52362

statistics for data AGU_LD subvolume (600 x 600 x 904)

statistics for data AGU_LD subvolume (600 x 600 x 904)
phase void clay quartz calcite
void
12260640 5476286 19764
clay 12260640
17604698 35225
quartz 5476286 17604698
304925
calcite 19764 35225 304925
sum 17756690 29900563 23385909 359914

statistics for data AGU_LD subvolume (1200 x 1200 x 904)

statistics for data AGU_LD subvolume (1200 x 1200 x 904)
phase void clay quartz calcite
void
52206124 23570468 118316
clay 52206124
76230640 191304
quartz 23570468 76230640
2128960
calcite 118316 191304 2128960
sum 75894908 128628068 101930068 2438580

statistics for data AGU_LTG_subvolume (352 x 352 x 301)

statistics for data AGU_LTG_subvolume (352 x 352 x 301)
phase void clay quartz calcite
void
2477578 5816 1
clay 2477578
2748643 0
quartz 5816 2748643
847
calcite 1 0 847
sum 2483394 5226221 2755306 848

statistics for data AGU_LTG_subvolume Low-res (93 x 93 x 80)

statistics for data AGU_LTG_subvolume Low-res
phase void clay quartz calcite
void
80921 29272 99
clay 80921
104471 221
quartz 29272 104471
475
calcite 99 221 475
sum 110292 185613 134218 795

statistics discussion

  1. The large domain data AGU_LD (1200 x 1200 x 1808) has the same resolution as small domain data AGU_SD – comparing to LTG data they are low-res
  2. AGU_LD is too complex to create a surface and do measurements in Avizo running on my desktop. But we can think that its subvolume and corresponding small domain data (AGU_SD) and its high res version (AGU_LTG) can be representable for the phase analysis
  3. High res data (LTG) reveals one more phase: feldspar
  4. High res data (LTG) reveals larger clay to void surface area ratio

Visualize Clay-void surface

The surface generated from the original data is about 7GB, Avizo’s “surface view” module crashes when rendering this large surface. So in order to show some visualization, we use “extract subvolume” module to extract a small portion of the original data and show a partial surface. The extracted subvolume is 300x300x300 lattice grid, the generated surface data is 773MB in size.

Here are some results:

  1. surface (red, mesh, clipped) show against orthoslice in xy direction

    _images/c-v-2.jpg

  2. surface (dark red, transparently shaded) show in rotated perspective view

    _images/c-v-3d-2.jpg _images/c-v-3d.jpg