- 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