Igor Pro procedures for analysis of microtubules in electron tomograms
The main procedure file is
- prepare separate
*.pxpfiles for each tomogram. See Note 1 and Note 2
MTLoader(), point Igor at the directory containing all pxps
- all files will load and be converted to properly formatted MT waves
BundleStats(). This will make heat maps for all MT bundles that were loaded. Note 3
- the resulting view is tiled. You can use
ShowMe()to simplify the view. See Note 4
PullOut()to analyse the angles of all MTs in the bundle. See Note 5
Compatible with IgorPro 6.3x and 7.0
An earlier version of this code, which predates this repo, was used in Nixon et al. 2015. This is reproduced as
Nixon2015Code.rtf a lexed version of the code for readability.
Two procedure files are included but not needed for analysis.
- Each MT is a 7 point wave named wave0,wave1,... Point 0 is the MT ID number 1,2,... Points 1-3 are the x,y,z, coordinates of the MT at the bottom of the tomogram. Points 4-6 are the x,y,z coordinates of the MT at the top of the tomogram.
- To use functions downstream, it is best to label your files logically. If there is control vs drug1 vs drug 2 and warm vs cold, i.e. 3 x 2 = 6 conditions; then label files logically. e.g. control_warm_2.pxp, drug1_cold_3.pxp
- In addition to the heatmaps and colour coded MT plots. A table is generated showing how many MTs per bundle, the area of a convex hull containing all MTs in a bundle and the resultant density.
- The input is a string containing wildcards to match the windows to be shown.
ShowMe("img_GFP*")will show all GFP heatmaps,
ShowMe("map_GFP*")will show all GFP colour coded MT maps.
ShowMe("*")will show everything.
- The procedure will do the rotation normalisation and make the waves to show the intersection of vectors with an XY plane at 100 nm in Z. Call using