Tomography Toolbox

Frequently asked Questions

Answers given to those questions are just tips, no complete solution to your problem. Maybe you run into further problems ... keep that in mind.

How to install Acquisition software ?

Tecnai 10
Tecnai 12
Tecnai F30/F20
Tecnai F30/G2 (Polara)
 

Can I use a CM300 ?

Not without any changes. But if you have the CM-Remote Library you can easily integrate this library into Matlab. You just need the header of the library to use the command loadlibrary.

Can I use a microscope without an energy filter ?

Not without any changes. There are two ways of solving this problem ether you build a "empty"  ActiveX-Server (Com) with dummy filter functions or you comment out all the commands with get(COMS.CCD,'Execute Script' ... in the following modules.

tom_center_slit.m:
tom_get_filter.m:
tom_get_state.m:
tom_make_acquisition_structure.m:
tom_set_state.m:

Can I use a microscope with a different Camera (and/or different Camera Inteface) ?

Not without any changes. You have to build your own camera ActiveX-Server or change the commands get(COMS.CCD set(COMS.CCD invoke(COMS.CCD which not control the filter. (COMS.CCD includes tecnaiccd.gatancamera ActiveX-Server which controls Camera and Filter) The commands controlling the filter ar e followed by a 'Execute Script'.

tom_acquire_acquisition.m:
tom_acquire_image.m:
tom_center_detail.m:
tom_center_slit.m:
tom_get_state.m:
tom_make_acquisition_structure.m:
tom_make_all_coms.m:
tom_set_filter.m:
tom_set_state.m:
tom_shift_calib_manual.m:
tom_stage_calib_manual.m:
tom_tiltaxis_calib_manual.m:
tom_update_header.m:

Tom_tilt_series does not start up (even though the software setup is the same)

There are 2 main reasons why tom_tilt_series is not starting up:

1: the WrapIUnknown.dll is not registered (error in tom_make_all_coms)

2: the hard coded path in the acquisition functions are not adapted. (error in tom_make_acquisition_structure)

For both reasons check Configuration Notes,
 

Matlap is busy and nothing happens.

One reason could be your hardware setup. If you don't have a double screen you have to change the window positions. (all commands with set(gcf,'position'....)

Check Use Acquisition with different hardware.

There are not all features visible on the GUI.

One reason could be that you use the wrong standard font. Try to change the font size from big to small.

The tom_makefun doesn't work.

One reason could be that your Current Directory is wrong. Change to the tom folder (where the tom_makefun is stored).  See also Configuration Notes.

Images are shifted by tom_volxy or images read with tom_emreadc are shifted .

One reason could be that you use the wrong C-compiler. Change the compiler with mex -setup.  See also Configuration Notes.

Tom_rec3d give an error message: Undefined function or variable 'ip'.

There was a bug in the first version of tom_rotate. To resolve this problem, ask us for the last version of tom_rotate or edit it and replace all the lines from line 39 to line 50 by

switch nargin
    case 4,
        center = varargin{4};
        ip=varargin{3};%bug fixed the 20th June 04
    case 3,
        ip=varargin{3};
        center = [ceil(size(varargin{1})./2)];%bug fixed for uneven dims - FF
    case 2,
        center = [ceil(size(varargin{1})./2)];%bug fixed FF
        ip = 'linear';
    otherwise
        disp('wrong number of Arguments');
        out=-1; return;
end;
 

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