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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Hello,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>I uploaded the GATAN dm3 file containing the image with a negative value to a pixel set, and found this to be the reference to the image: QA Bug | 9526 (new).<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Let me take the chance and add some further, important observations I did today:<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>I found , that going in FiJi the following way, then the data import works correctly for my dm3 with a negative value stored for a pixel:<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Import </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Bio-Formats<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>After selecting the file of interest, a dialog window "Bio-Formats Import Options" appears, and having answered the default settings the import does work correctly! This Options dialog appears always again if importing a dm3 file.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>But, if only importing in FiJi data in the following way, then the bug appears the same as it appears using the MATLAB front end for the Bio-Formats import function ‘bfopen’:<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Open…<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>does not work correctly.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>Apparently, the FiJi "File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Open…" path uses some identical step as the MATLAB /Bio-Formats command 'bfopen' does, while the "File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Import </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Bio-Formats" path does something different which works flawless.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>I for sure downloaded and installed and use this MATLAB toolbox for using Bio-Formats in MATLAB and believe to have the older LOCI things deleted:<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>I further believe to remember correctly that I downloaded and installed FiJi, and somehow remember that there was something about ImageJ2 support, which I for sure didn´t reject, whatever it was. If there has been any choice to get FiJi in different versions, then I believe I decided for the FiJi with version ImageJ2 in use. I remember quite well that I decided to not install ImageJ and LOCI plugin anymore but to install for convenience the all-inclusive package FiJi, because I read that then the LOCI bioformats would be integrated, and FiJi update mechanism would also update that bioformats part then.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>I am now confused to have seen somewhere on the screen (not sure if it actually was in FiJI or MATLAB), that some SCIFIO is somewhere in use or has been mentioned in a message when opening / importing a dm3 file. I am further confused because I thought to have read somewhere that if the LOCI plugin would be installed that then ImageJ would automatically use it in the standard "File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Open…" path if needed. I am completely confused if I am actually using now the LOCI plugin in ImageJ, or the OME Bio-Formats import filter, or some SciFio thing or whatever, but this should not be the topic here in my bug report.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'>In summary: for sure the MATLAB 'bfopen' command does not produce the correct result, and the FiJi "File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Open…" menu neither, but the FiJi "File </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Import </span><span style='font-size:8.5pt;font-family:Wingdings'>à</span><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'> Bio-Formats" menu apparently works correctly.<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:8.5pt;font-family:"MS Shell Dlg 2","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='color:#1F497D'>Best greetings from the EM-Labs of CIC biomaGUNE,<o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='color:#1F497D'>Marco Möller<o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'>----------------------------------------------------------------<o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'>Marco Möller<o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='font-size:8.0pt;color:#1F497D'>Platform Manager - Electron Microscopy<o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='font-size:4.0pt;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=ES style='font-size:8.0pt;color:#1F497D'>CIC biomaGUNE<o:p></o:p></span></b></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'>Parque Tecnológico de San Sebastián<o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'>Paseo Miramón, 182. Ed. Empresarial C<o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='font-size:8.0pt;color:#1F497D'>20009 San Sebastián (Guipúzcoa)</span><span lang=ES style='font-size:8.0pt;color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'>SPAIN<o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:8.0pt;color:#1F497D'>Tel: +34 943 00 53 25<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><a href="mailto:mmoller@cicbiomagune.es"><span style='font-size:8.0pt'>mmoller@cicbiomagune.es</span></a></span><span style='font-size:8.0pt;color:#1F497D'><o:p></o:p></span></p></div><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Balaji Ramalingam [mailto:b.ramalingam@dundee.ac.uk] <br><b>Sent:</b> Tuesday, September 09, 2014 2:54 PM<br><b>To:</b> Marco Moller; ome-devel@lists.openmicroscopy.org.uk<br><b>Subject:</b> Re: [ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>Hi Marco,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>Thank you for your detailed summary.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>As suggested, it would be great if you could upload the file to the following URL,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><a href="https://www.openmicroscopy.org/qa2/qa/upload">https://www.openmicroscopy.org/qa2/qa/upload</a>/<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>We will then create a ticket, post investigation and CC you on the same.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>Thanks again,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>Best,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'>Balaji<o:p></o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:10.5pt;color:#282828;background:white'>__________________</span><span style='font-size:10.5pt;color:#282828'><o:p></o:p></span></p></div><div><p style='margin:0cm;margin-bottom:.0001pt'><span style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:#282828'>Mr Balaji Ramalingam<o:p></o:p></span></p><p style='margin:0cm;margin-bottom:.0001pt'><span style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:#282828'>Software Developer<o:p></o:p></span></p><p style='margin:0cm;margin-bottom:.0001pt'><span style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:#282828'>OME Team<o:p></o:p></span></p><p style='margin:0cm;margin-bottom:.0001pt'><span style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:#282828'>College of Life Sciences<o:p></o:p></span></p><p style='margin:0cm;margin-bottom:.0001pt'><span style='font-size:10.5pt;font-family:"Calibri","sans-serif";color:#282828'>University of Dundee<o:p></o:p></span></p></div></div></div></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='color:black'>From: </span></b><span style='color:black'>Marco Moller <<a href="mailto:mmoller@cicbiomagune.es">mmoller@cicbiomagune.es</a>><br><b>Date: </b>Tuesday, 9 September 2014 08:22<br><b>To: </b>"<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br><b>Subject: </b>[ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.5pt;color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span style='color:black'>Hello,<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>I found a bug in the current BIOFORMATS import filter for GATAN *.dm3 (Electron Microscopy) files:<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>If the original GATAN software stored for a pixel in the image a negative value, then the BIOPFRORMATS import filter does not read this out correctly, but changes the negative value to an extreme high positive value.<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>I am working with MATLAB and have not much experience with ImageJ, but at least could confirm that this does not only happen with the MATLAB front end ‘bfopen’ of the BIOFORMATS import filter, but also happens when importing such image containing a negative value to ImageJ by the BIOFORMATS import filter used there.<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>I work on WinXP 32-bit or Win7 64-bit, have FiJi, MATLAB and BIOFORMATS software all in the most up to date version (as of 8 September 2014) installed.<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Please have a look on the following little log on querying the max and min pixel value found in the image by different software:<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span lang=DE style='color:black'>Gatan Digital Micrograph V1.85 (32-bit):</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>GATAN_IMAGE: Minimum -93 at (1920,612)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>GATAN_IMAGE: Maximum 1320 at (2035,135)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Gatan Microscopy Suite Digital Micrograph V2.02.800.0 (32-bit):<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>GATAN_IMAGE: Minimum -93 at (1920,612)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>GATAN_IMAGE: Maximum 1320 at (2035,135)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>MATLAB (64-bit), using BIOFORMATS command ‘bfopen’<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>max = 4294967203 at (613,1921)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>min = 45 at (1722,407)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>after changing manually the (in MATLAB max, in GATAN negative) value to i.e. 1000 using MATLAB command GATAN_IMAGE(613,1921) = 1000, applying ‘bfopen’ in MATLAB shows:<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>max: 1320 at (136,2036)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>min: 45 at(1722,407) (which is correct, this I confirmed to before have been the second smallest value in the file)<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Checking if this is a ‘bfopen’ behavior or a general BIOFROMATS behavior:<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>FiJi (64-bit), using the BIOFORMATS import option:<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>min: 45<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>max: 4,29E+09<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>I would be willing to share the GATAN image file of interest, but prefered not to attach it to the e-mail to the mailing list. If anyone would have interest in the image, please contact me and I can send it then to the interested person(s).<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>As I am meanwhile using the really excellent dm3 import filter written for MATLAB by Andreas Korinek (<a href="http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader">http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader</a>), which I recommend you to have a look at in order to find much information about the dm3 file structure (much more data is extracted from dm3 than by the present BIOFORMATS filter), my e-mail to the developer list does not ask for your explicit answer. Instead it is cordially meant to just support the BIOFORMATS project by the given information and bug report.<o:p></o:p></span></p><p class=MsoNormal><span style='color:black'>Best greetings from the EM-Labs of CIC biomaGUNE,<o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='color:black'>Marco Möller</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'>----------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'>Marco Möller</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='font-size:8.0pt;color:black'>Platform Manager - Electron Microscopy</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES style='font-size:4.0pt;color:black'> </span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><b><span lang=ES style='font-size:8.0pt;color:black'>CIC biomaGUNE</span></b><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'>Parque Tecnológico de San Sebastián</span><span style='color:black'><o:p></o:p></span></p><p class=MsoNormal><span lang=ES-TRAD style='font-size:8.0pt;color:black'>Paseo Miramón, 182. Ed. 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