Avizo tutorial

  • TLD — through lease detector
  • tiff generated with FIB software has lots of important information in the header >> except for step size
  • ‘open data’ >> pick folder that your data is and select all images
    • they’ll all be numerically sequenced
  • important FEI SEM TIFF — this is where you select a thickness
  • make sure the voxel size is as close to a cube as you can
  • there’s a check box for a wizard, right now we’re going to do it manually, then we’ll go back and talk about what the wizard would have done automatically
  • volume of data, the stack, is the green object
  • window default >> if you accidentally x out of the properties
  • spin animation — right click, preferences, spin animation
  • alignment — most people do this first, and then crop the unwanted data
  • crop to remove unwanted/bad data
  • histogram — color map
  • clip — when you don’t want to delete it, but you just don’t want to show it, especially important for movies
  • filtering — takes pixels, makes them average if outlier
  • bounding box >> create — just shows a wireframe box around all the relevant data
  • .am is the project file
  • geometry transforms >> align slices
  • align slices, shows up as an operation in the project window
  • least squares alignments
  • align >> options >> TURN OFF ‘ALLOW ROTATION’ — must do every time
  • align slices >> action >> edit >> align all
  • **filter sandbox** — allows you to apply a filter to a smaller subset of the picture
  • non local means filter — most common
    • search window px — higher, more aggressive
    • similarity index — higher, more aggressive
  • filter sandbox — allows a preview, but when you hit apply, that’s for the whole data set
  • saving
    • you save individual data sets
    • then when you get to movies/extra stuff, then you start saving it as a project
  • edit new label field
  • volren, volume rendering — some archaic difference, choose volren
  • isosurface rendering
  • save project
    • minimize project size
    • minimize project computation
  • turn volren off — still bits left over — that has something to do with the threshold
  • try and find out how to figure out the reduced density
  • edit new label field == segmentation
  • magic wand, blow tool — hard way, literally drawing it out
  • threshold tool — easiest way to segment, click the ‘all slices’ check box
  • go back to the project
  • right click on filtered labels >> generate surface >> apply
  • now we have .surf, now we want to create surface view
  • buffer >> remove/clear/remove
  • materials >> pore, pore

tomorrow — talk about FIB wizard, teddy bear tutorial, then reconstruct this

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