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#12 Loading 16bit images as Amira files into MIB error

Fixed
nobody
None
2018-12-19
2018-01-08
Kevin Loftis
No

Hello,

MIB is throwing an error when I try to load 16bit volume as an Amira file. MIB allows me to import volumes as Amira files when they are 8bit, but breaks when I try to import 16bit volumes. Here is the error that I am reciveing from the MATLAB console.

Index exceeds matrix dimensions.

Error in getAmiraMeshHeader (line 89)
parField = [parField '_' tline(1:spaces(1)-1)];

Error in mibGetImageMetadata (line 324)
[~, info, dim_xyczt] = getAmiraMeshHeader(files(fn_index).filename);

Error in mibLoadImages (line 69)
[img_info, files, pixSize] = mibGetImageMetadata(filenames, options); % get
meta data for the datasets

Error in mibController/mibFilesListbox_Callback (line 56)
[img, img_info, pixSize] = mibLoadImages(cellstr(fn), options);

Error in mibGUI>mibFilesListbox_Callback (line 626)
handles.mibController.mibFilesListbox_Callback();

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in mibGUI (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)mibGUI('mibFilesListbox_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

I am running the Matlab version of MIB ver 2.211 using a Windows 7 operating system.

Thank you,
Kevin

Related

Tickets: #12

Discussion

  • Ilya Belevich

    Ilya Belevich - 2018-01-08

    Hi Kevin,
    the problem comes from the amira mesh file header. Could you please open the file in a text editor and send me the header - it is a plain text section in the beginning of the file, before binaries.
    Thanks!

    Ilya

     

    • Kevin Loftis

      Kevin Loftis - 2018-01-08

      Hi Ilya,

      Thank you for the quick reply. Here is the header from the file.

      AmiraMesh BINARY-LITTLE-ENDIAN 2.1

      define Lattice 2883 738 1395

      Parameters {
      Units {
      Coordinates "nm"
      }
      HistoryLogHead {
      HistoryLog {
      UID:52104d24-2b49-489b-acaf-731eb7834361 {
      Module:Deblur {
      Connection:inputImage {
      UID "a4f4aed5-f882-4383-8664-833811fc6317"
      }
      Parameter:interpretation "1",
      Parameter:sharpeningFactor "2",
      ResultNumber "0",
      Label "Deblur",
      ResourceKey "deblur",
      ModuleState "create deblur \"Deblur\"
      \"Deblur\" setIconPosition 312 535
      \"Deblur\" setVar \"CustomHelp\" {deblur.html}
      \"Deblur\" interpretation setValue 1
      \"Deblur\" outputLocation setIndex 0 0
      \"Deblur\" inputImage connect \"MCF7-ICD-0034.filtered.Sheared\"
      \"Deblur\" sharpeningFactor setMinMax 0 0 3.40282346638529e+038
      \"Deblur\" sharpeningFactor setValue 0 2
      \"Deblur\" applyTransformToResult 1
      \"Deblur\" fire
      \"Deblur\" setViewerMask 16383
      \"Deblur\" select
      \"Deblur\" setPickable 1
      "
      }
      Product "Amira",
      Version "6.4",
      Date "2017-12-19T09:45:05",
      Room "HxWorkroomMain"
      }
      UID:a4f4aed5-f882-4383-8664-833811fc6317 {
      Module:Shear {
      Connection:data {
      UID "4239c4f9-9b20-4edb-91d6-aa12cb14c05f"
      }
      Parameter:info "",
      Parameter:angle "-13",
      Parameter:background "4",
      ResultNumber "0",
      Label "Shear",
      ResourceKey "HxShear",
      ModuleState "create HxShear \"Shear\"
      \"Shear\" setIconPosition 316 442
      \"Shear\" setVar \"CustomHelp\" {HxShear}
      \"Shear\" data connect \"MCF7-ICD-0034.filtered.am\"
      \"Shear\" fire
      \"Shear\" angle setMinMax 0 -90 90
      \"Shear\" angle setValue 0 -13
      \"Shear\" background setMinMax 0 4 232
      \"Shear\" background setValue 0 4
      \"Shear\" applyTransformToResult 1
      \"Shear\" fire
      \"Shear\" setViewerMask 16383
      \"Shear\" select
      \"Shear\" setPickable 1
      "
      }
      Product "Amira",
      Version "6.4",
      Date "2017-12-19T09:36:37",
      Room "HxWorkroomMain"
      }
      UID:4239c4f9-9b20-4edb-91d6-aa12cb14c05f {
      Module:GaussianFilter {
      Connection:inputImage {
      UID "a4c8c20c-3170-4072-964d-8fa488334cc5"
      }
      Parameter:interpretation "1",
      Parameter:kernelType "0",
      Parameter:standardDeviationX "2",
      Parameter:standardDeviationY "2",
      ResultNumber "0",
      Label "Gaussian Filter",
      ResourceKey "gaussianfilter",
      ModuleState "create gaussianfilter \"Gaussian Filter\"
      \"Gaussian Filter\" setIconPosition 375 243
      \"Gaussian Filter\" setVar \"CustomHelp\" {gaussianfilter.html}
      \"Gaussian Filter\" interpretation setValue 1
      \"Gaussian Filter\" outputLocation setIndex 0 0
      \"Gaussian Filter\" inputImage connect \"MCF7-ICD-0034.png\"
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" kernelType setIndex 0 0
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" standardDeviationX setMinMax 0 0 3.40282346638529e+038
      \"Gaussian Filter\" standardDeviationX setValue 0 2
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" standardDeviationY setMinMax 0 0 3.40282346638529e+038
      \"Gaussian Filter\" standardDeviationY setValue 0 2
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" kernelSize setMinMax 0 0 2147483648
      \"Gaussian Filter\" kernelSize setValue 0 9
      \"Gaussian Filter\" kernelSize setMinMax 1 0 2147483648
      \"Gaussian Filter\" kernelSize setValue 1 9
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" autoScale setIndex 0 1
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" applyTransformToResult 1
      \"Gaussian Filter\" fire
      \"Gaussian Filter\" setViewerMask 16383
      \"Gaussian Filter\" select
      \"Gaussian Filter\" setPickable 1
      "
      }
      Product "Amira",
      Version "6.4",
      Date "2017-12-18T11:04:51",
      Room "HxWorkroomMain"
      }
      UID:a4c8c20c-3170-4072-964d-8fa488334cc5 {
      OriginalFile {
      LoadCommand "load -unit nm -png +box 0 24568 0 16376 0 11152 +mode 100 \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0034.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0035.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0036.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0037.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0038.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0039.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0040.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0041.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0042.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0043.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0044.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0045.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0046.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0047.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0048.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0049.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0050.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0051.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0052.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0053.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0054.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0055.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0056.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0057.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0058.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0059.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0060.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0061.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0062.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0063.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0064.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0065.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0066.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0067.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0068.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0069.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0070.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0071.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0072.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0073.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0074.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0075.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0076.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0077.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0078.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0079.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0080.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0081.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0082.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0083.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0084.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0085.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0086.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0087.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0088.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0089.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0090.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0091.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0092.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0093.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0094.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0095.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0096.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0097.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0098.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0099.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0100.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0101.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0102.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0103.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0104.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0105.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0106.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0107.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0108.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0109.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0110.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0111.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0112.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0113.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0114.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0115.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0116.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0117.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0118.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0119.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0120.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0121.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0122.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0123.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0124.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0125.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0126.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0127.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0128.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0129.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0130.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0131.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0132.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0133.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0134.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0135.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0136.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0137.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0138.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0139.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0140.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0141.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0142.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0143.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0144.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0145.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0146.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0147.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0148.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0149.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0150.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0151.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0152.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0153.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0154.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0155.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0156.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0157.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0158.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0159.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0160.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0161.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0162.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0163.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0164.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0165.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0166.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0167.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0168.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0169.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0170.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0171.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0172.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0173.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0174.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-0175.png\" 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\"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1361.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1362.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1363.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1364.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1365.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1366.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1367.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1368.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1369.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1370.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1371.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1372.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1373.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1374.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1375.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1376.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1377.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1378.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1379.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1380.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1381.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1382.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1383.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1384.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1385.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1386.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1387.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1388.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1389.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1390.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1391.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1392.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1393.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1394.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1395.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1396.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1397.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1398.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1399.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1400.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1401.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1402.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1403.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1404.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1405.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1406.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1407.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1408.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1409.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1410.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1411.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1412.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1413.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1414.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1415.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1416.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1417.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1418.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1419.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1420.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1421.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1422.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1423.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1424.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1425.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1426.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1427.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1428.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1429.png\" \"Z:/EM/EM_Data/MCF7_cells/Sunjong_MCF7_DAPI_Registered/MCF7-ICD-1430.png\"",
      Filename "MCF7-ICD-0034.png"
      }
      Product "Amira",
      Version "6.4",
      Date "2017-12-18T10:55:38",
      Room "HxWorkroomMain"
      }
      CurrentUID "52104d24-2b49-489b-acaf-731eb7834361"
      }
      }
      Content "2883x738x1395 short, uniform coordinates",
      BoundingBox 1168 24224 5112 11008 0 11152,
      CoordType "uniform"
      }

      Lattice { short Data } @1

      Data section follows

      Thank you,
      Kevin

      From: Ilya Belevich [mailto:ajaxel@users.sf.net]
      Sent: Monday, January 08, 2018 1:14 PM
      To: [im-browser:tickets]
      Subject: [im-browser:tickets] #12 Loading 16bit images as Amira files into MIB error

      Hi Kevin,
      the problem comes from the amira mesh file header. Could you please open the file in a text editor and send me the header - it is a plain text section in the beginning of the file, before binaries.
      Thanks!

      Ilya

      [tickets:#12]https://sourceforge.net/p/im-browser/tickets/12/ Loading 16bit images as Amira files into MIB error

      Status: New
      Created: Mon Jan 08, 2018 07:14 PM UTC by Kevin Loftis
      Last Updated: Mon Jan 08, 2018 07:14 PM UTC
      Owner: nobody

      Hello,

      MIB is throwing an error when I try to load 16bit volume as an Amira file. MIB allows me to import volumes as Amira files when they are 8bit, but breaks when I try to import 16bit volumes. Here is the error that I am reciveing from the MATLAB console.

      Index exceeds matrix dimensions.

      Error in getAmiraMeshHeader (line 89)
      parField = [parField '_' tline(1:spaces(1)-1)];

      Error in mibGetImageMetadata (line 324)
      [~, info, dim_xyczt] = getAmiraMeshHeader(files(fn_index).filename);

      Error in mibLoadImages (line 69)
      [img_info, files, pixSize] = mibGetImageMetadata(filenames, options); % get
      meta data for the datasets

      Error in mibController/mibFilesListbox_Callback (line 56)
      [img, img_info, pixSize] = mibLoadImages(cellstr(fn), options);

      Error in mibGUI>mibFilesListbox_Callback (line 626)
      handles.mibController.mibFilesListbox_Callback();

      Error in gui_mainfcn (line 95)
      feval(varargin{:});

      Error in mibGUI (line 42)
      gui_mainfcn(gui_State, varargin{:});

      Error in
      matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)mibGUI('mibFilesListbox_Callback',hObject,eventdata,guidata(hObject))
      Error while evaluating UIControl Callback.

      I am running the Matlab version of MIB ver 2.211 using a Windows 7 operating system.

      Thank you,
      Kevin

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/im-browser/tickets/12/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Tickets: #12

      alternate

      • Ilya Belevich

        Ilya Belevich - 2018-01-09

        Hi Kevin,
        let me know if the new functions, fixed the problem.
        Ilya

         

  • Ilya Belevich

    Ilya Belevich - 2018-01-09

    Hi Kevin,
    you have quite sofisticated header in the AmiraMesh file. What was the program that generated the file?

    I modified reading functions for AmiraMesh files: now they can read those fields. But MIB won't use them and the saving of files to the AmiraMesh format won't save them as well. But hopefully, you will be able to read the files.
    Please update, the following functions attached to this message:
    1. MIB2\ImportExportTools\Amira\amiraMesh2bitmap.m
    2. MIB2\ImportExportTools\Amira\getAmiraMeshHeader.m

    Best regards,
    Ilya

     
    amiraMesh2bitmap.m
    getAmiraMeshHeader.m

  • Ilya Belevich

    Ilya Belevich - 2018-12-19
    • status: New --> Fixed
     

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