imodinfo(1) General Commands Manual imodinfo(1)NAMEimodinfo - Prints information about IMOD files.SYNOPSISimodinfo [options] IMOD_filenameDESCRIPTIONPrints information about an IMOD model to standard output. The types of information output vary, depending upon the options. Typical uses include printing out lists of objects, contours and point data in an IMOD file; printing out areas, lengths and centroids of contours; and printing out surface areas and volumes of objects or surfaces. The measurements of lengths, areas, and volumes are generally expressed in terms of the units of the pixel size defined in the model header (e.g., nm or microns), if one is defined. A Z-scale in the model header is also applied as appropriate. However, reported positions are always in pixels. The program computes surface area and volume in several different ways, depending upon whether an object is meshed or not: 1) If there is no mesh information, volume is computed by taking the area of each contour times the thickness of the sections (defined by pixel size and Z-scale), summed over all of the contours. This is referred to as cylinder volume. It will be inaccurate if you skipped sections in modeling, especially if you skipped sections routinely. Other than this, it will be very close to correct. 2) If there is no mesh information, surface area is computed by taking the length of each contour times the section thickness, summed over all contours. This is referred to as cylinder surface area and it is grossly inaccurate. 3) With mesh information, the program determines which contours are connected to other contours or to cap points by a mesh, and sums the area of contours times the distance to the connected contours in Z. This measure is now referred to as the contour volume. (It used to be referred to as mesh volume because it uses mesh information, even though it is not the volume inside the mesh.) It handles the problem of skipped sections and also gives a slightly more accurate volume mea- surement for the capped regions because it integrates with a trape- zoidal approximation. This computation is valid only for closed con- tour, planar objects. 4) With a mesh, the program also computes a volume from the mesh by summing the volumes of tetrahedra formed between each mesh triangle and a single point at the center of the mesh. This is referred to as the volume inside the mesh. It will be slightly more accurate than the contour volume if the mesh completely encloses the volume, but it can be quite inaccurate if the mesh is not capped. This computation is valid for any fully meshed volume, including tubular meshes around an open contour, as well as saved isosurface objects. Such a volume can be computed for each surface if the option to use surface information was used when meshing. 5) With a mesh, surface area is computed by adding the areas of all the triangles in the mesh. This is referred to as mesh surface area and it is an exact measure of the area of the mesh. However, to the extent that the mesh is not smooth, it can overestimate the true surface area of the object. If any of your model objects has complex topology, with contours inside of other contours, the computed volumes will not be correct unless the program analyzes for inside contours, which it does not do by default. Use-ioption to have the program do this analysis. However, if you use-xor-yto specify a subset range in X or Y, or use-tto restrict the analysis with clipping planes, the inside-contour analysis is done automatically and you do not need to specify-iseparately. With these other options, the program will give the same outputs as with the-ioption. The options-a,-c,-e,-l,-L,-F,-p,-rand-sare mutually exclusive.OPTIONS-aPrint ascii readable IMOD output. Not all of the types of data stored in a binary model are printed in an ascii model file, but all contour and mesh data are printed. Also, slicer angles, clipping planes, and general values assigned to contours and points will be printed.-cPrint volume, surface area, and center of gravity for each object in column output. For closed contour objects, the cen- troid is computed from the area enclosed inside each contour. For open contour objects, the centroid is computed from the line segments themselves.-lPrint lengths of open contours in column output.-LPrint lengths of contours broken out by fine-grained color, if any, and excluding gaps. For each object, a table is printed for each color used. This table shows the contour number and the length of the portion assigned that color, for each contour that uses the color. If the-hoption is given, only summary information on total and mean lengths os printed. Unlike in other length reports, this one excludes gaps from the total length, so this option is useful for getting correct lengths of what is drawn when there are gaps, even if there are no fine- grained colors.-sPrint volumes and surface areas for each separate surface in an object, as defined by contour surface numbers and possibly by mesh surface numbers. The maximum extent, or biggest distance between any two points in the surface contours, is also reported. If a mesh is available, the cylinder surface area is omitted from the report. If any meshes have a surface number greater than 0, the volume inside the mesh (mesh volume) will be reported for each surface. If such information seems to be available for all surfaces, the cylinder volume will be omitted. To get mesh volumes, be sure to cap and to select the option to use surface information when meshing.-pPrint point size information, including a summary of mean radius, and the implied total surface area and volume of scat- tered points. There will be a size output for every point in any contour that has points with non-zero size. If there is a default point size for the object, that size will be listed when there is no size defined for an individual point. These sizes will be in the model units. Note that the ascii model output will also show point sizes in pixels for each point that has one defined.-rPrint ratio of length to area for closed contours.-ePrint properties of equivalent ellipses for closed contours. The equivalent ellipse is the one with the same second moments as the area enclosed by a contour. If limits are entered with-x,-y, or-z, only contours with center coordinates within the limits are in reported. Only the X and Y coordinates of the points are considered when computing these ellipses. For each contour, the values reported are the X and Y center coordinates of the ellipse (i.e, the centroid of the contour area), the average Z coordinate of the contour points, all in pixels, the semi-major and semi-minor axes in scaled units, the eccentricity as usually defined (a value between 0 for a circle and 1 for a maximally elongated ellipse), and the angle of the semi-major axis (a value between 0 and 180 except as described next). If the range of angles is less than 80 degrees, then numbers will be reported that are suitable for simple averaging. This is accomplished based on the angle of the first contour for an object: if it is less than 44, then all subsequent angles greater than 136 will have 180 subtracted to give negative angles; if it is greater than 136, 180 is then added to angles less than 45. Means and standard deviations are also reported for these four measures; the mean of the angles will be adjusted to be between 0 and 180. BEWARE: if the range of angles is greater than 88 degrees, the mean will be meaningless unless the distribution of angles does not wrap around at 0 or 180, so you need to examine the individual angles before using the mean.-FPrint full report on the objects, a collection of summary infor- mation.-olistPrint data only from the objects given in the list, a comma-sep- arated list of ranges.-iAnalyze for inside contours and adjust computed volume by sub- tracting rather than adding the areas of contours that represent inside-out surfaces. This option works only for closed con- tours. It is invoked automatically if you analyze a subset in X or Y, or use clipping planes. Individual contour data will not be printed for closed contour objects.-xmin,max-ymin,max-zmin,maxCompute areas and volumes within the subvolume specified by the minimum and maximum values. One or two of these three options may be entered if desired. Subvolume analysis works only with closed contour and scattered point objects. It works for options that print surface areas and volumes and with the-poption. In the standard output, the number of scattered points within the subvolume will be reported for each object.-t1/-1Truncate objects by their respective clipping planes; enter-t1or-t-1to use region shown or not shown by the clipping planes, respectively. All currently active object clipping planes will be applied, as well as any active global clipping planes for objects that do not have the setting to skip the global planes. Like the subvolume analysis, this option works only with closed contour and scattered point objects, and for options that print surface areas and volumes and with the-poption. Clipping plane truncation can be used together with subvolume analysis.-v[v]Print more verbose output. The-vvoption will increase the level of output information even further. These options over- ride the-hoption.-hSuppress the information about each contour in the standard model output. Use this option to extract summary information more easily from large models.-ffilenameWrite output to given filename instead of to standard output.AUTHORSJim Kremer David MastronardeSEEALSO3dmodBUGSCylinder surface areas are erroneous because they do not account for the obliquity of the surface; for a sphere the area will be underesti- mated by 22%. Use mesh surface areas whenever possible. Email bug reports to mast at colorado dot edu. IMOD 4.10.28 imodinfo(1)