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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText>Dear Greg, Dear Curtis,<o:p></o:p></p><p class=MsoPlainText>Sorry for not having answered before in more detail to your comments. I am a MATLAB user and only occasionally use ImageJ and therefore do not find all technical information of interest in ImageJ as quick.<o:p></o:p></p><p class=MsoPlainText>Well, now I found more information, following your guidance in your comments:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>> ImageJ2 uses SCIFIO (SCientific Image Format Input and Output) by default for most image input tasks. You can change this behavior at any time by running Edit > Options > ImageJ2 and modifying the Use SCIFIO when opening files option. <o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I confirm you, that for using the command "FILE > OPEN... " the error occurs with SCIFIO feature enabled in that configuration menu, and that the error does not occur anymore since I disabled the use of SCIFIO in that configuration menu.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>The error occurs in MATLAB (2014a) using 'bfopen' from this package:<o:p></o:p></p><p class=MsoPlainText><a href="http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip">http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip</a><o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>By the way,<o:p></o:p></p><p class=MsoPlainText>the error occurs in MATLAB independent of having added a "static path" to "bioformats_package.jar" with having configured in the bfopen.m file "autoloadBioFormats = 0;" , or using the "dynamic path" option with "autoloadBioFormats = 1;" .<o:p></o:p></p><p class=MsoPlainText>Although not expecting the following error message to be linked to the reported bug with the dm3 file, I will mention it now anyway, for the case I would be wrong to not mention it. The first time calling the 'bfopen' command in a MATLAB session produces the following warning message:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>"<o:p></o:p></p><p class=MsoPlainText>SLF4J: Class path contains multiple SLF4J bindings.<o:p></o:p></p><p class=MsoPlainText>SLF4J: Found binding in [jar:file:/C:/Program%20Files/MATLAB/R2014a/java/jarext/slf4j/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]<o:p></o:p></p><p class=MsoPlainText>SLF4J: Found binding in [jar:file:/C:/Program%20Files/BIOFORMATS/bioformats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]<o:p></o:p></p><p class=MsoPlainText>SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.<o:p></o:p></p><p class=MsoPlainText>"<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>This SLF4J error message does not appear if using the dynamic binding.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Some tiny part of the full information about this SLF43J error given on the mentioned SLF4J website :<o:p></o:p></p><p class=MsoPlainText>"The warning emitted by SLF4J is just that, a warning. Even when multiple bindings are present, SLF4J will pick one logging framework/implementation and bind with it. The way SLF4J picks a binding is determined by the JVM and for all practical purposes should be considered random."<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I so far just ignore the warning message, because I couldn't conclude how to really solve that SLF4J problem in MATLAB, neither by the information given on the SLF4J website. However, I mention it now here, because I might be wrong with my unreliable opinion that it shouldn´t affect the dm3 read out. Who knows, sometimes computer system show very obscure behaviours. So, better you know about it this message now, too.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Best greetings from the EM-Labs of CIC biomaGUNE,<o:p></o:p></p><p class=MsoPlainText><span lang=ES>Marco<o:p></o:p></span></p><p class=MsoPlainText><span lang=ES><o:p> </o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>-----Original Message-----<br>From: Dr Gregory Jefferis [mailto:jefferis@mrc-lmb.cam.ac.uk] <br>Sent: Wednesday, September 10, 2014 11:17 PM<br>To: Marco Moller<br>Cc: OME-devel mailing list; Curtis Rueden<br>Subject: Re: [ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Dear Marco,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Given Curtis' point below, it would be to check that this is not in the<o:p></o:p></p><p class=MsoPlainText>DM3 reader bundled with Fiji (which I wrote).<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><a href="http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html"><span style='color:windowtext;text-decoration:none'>http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html</span></a><o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>If you send me your file, I can check.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Best wishes,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Greg Jefferis.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>On 9 Sep 2014, at 20:00, Curtis Rueden wrote:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>> Hi Marco,<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>>> Apparently, the FiJi "File > Open…" path uses some identical step as <o:p></o:p></p><p class=MsoPlainText>>> the MATLAB /Bio-Formats command 'bfopen' does, while the "File > <o:p></o:p></p><p class=MsoPlainText>>> Import > Bio-Formats" path does something different which works <o:p></o:p></p><p class=MsoPlainText>>> flawless.<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> There are several different scenarios:<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> 1) Fiji's File > Open with SCIFIO disabled [1]<o:p></o:p></p><p class=MsoPlainText>> 2) Fiji's File > Open with SCIFIO enabled<o:p></o:p></p><p class=MsoPlainText>> 3) File > Import > Bio-Formats<o:p></o:p></p><p class=MsoPlainText>> 4) The MATLAB bfopen script<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> In case (1), Fiji will use a bundled DM3 reader plugin [2], which <o:p></o:p></p><p class=MsoPlainText>> takes precedence over Bio-Formats.<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> In cases (2), (3) and (4), Bio-Formats will be used.<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> Regards,<o:p></o:p></p><p class=MsoPlainText>> Curtis<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> [1] <a href="http://imagej.net/SCIFIO"><span style='color:windowtext;text-decoration:none'>http://imagej.net/SCIFIO</span></a><o:p></o:p></p><p class=MsoPlainText>> [2]<o:p></o:p></p><p class=MsoPlainText>> <a href="https://github.com/fiji/IO/blob/master/src/main/java/io/DM3_Reader.jav"><span style='color:windowtext;text-decoration:none'>https://github.com/fiji/IO/blob/master/src/main/java/io/DM3_Reader.jav</span></a><o:p></o:p></p><p class=MsoPlainText>> a<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>> On Tue, Sep 9, 2014 at 11:46 AM, Marco Moller <o:p></o:p></p><p class=MsoPlainText>> <<a href="mailto:mmoller@cicbiomagune.es"><span style='color:windowtext;text-decoration:none'>mmoller@cicbiomagune.es</span></a>><o:p></o:p></p><p class=MsoPlainText>> wrote:<o:p></o:p></p><p class=MsoPlainText>><o:p> </o:p></p><p class=MsoPlainText>>> Hello,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I uploaded the GATAN dm3 file containing the image with a negative <o:p></o:p></p><p class=MsoPlainText>>> value to a pixel set, and found this to be the reference to the <o:p></o:p></p><p class=MsoPlainText>>> image: QA Bug |<o:p></o:p></p><p class=MsoPlainText>>> 9526 (new).<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Let me take the chance and add some further, important observations I <o:p></o:p></p><p class=MsoPlainText>>> did<o:p></o:p></p><p class=MsoPlainText>>> today:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I found , that going in FiJi the following way, then the data import <o:p></o:p></p><p class=MsoPlainText>>> works<o:p></o:p></p><p class=MsoPlainText>>> correctly for my dm3 with a negative value stored for a pixel:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> File à Import à Bio-Formats<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> After selecting the file of interest, a dialog window "Bio-Formats <o:p></o:p></p><p class=MsoPlainText>>> Import<o:p></o:p></p><p class=MsoPlainText>>> Options" appears, and having answered the default settings the import <o:p></o:p></p><p class=MsoPlainText>>> does<o:p></o:p></p><p class=MsoPlainText>>> work correctly! This Options dialog appears always again if importing <o:p></o:p></p><p class=MsoPlainText>>> a dm3<o:p></o:p></p><p class=MsoPlainText>>> file.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> But, if only importing in FiJi data in the following way, then the <o:p></o:p></p><p class=MsoPlainText>>> bug<o:p></o:p></p><p class=MsoPlainText>>> appears the same as it appears using the MATLAB front end for the<o:p></o:p></p><p class=MsoPlainText>>> Bio-Formats import function ‘bfopen’:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> File à Open…<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> does not work correctly.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Apparently, the FiJi "File à Open…" path uses some identical step <o:p></o:p></p><p class=MsoPlainText>>> as the<o:p></o:p></p><p class=MsoPlainText>>> MATLAB /Bio-Formats command 'bfopen' does, while the "File à Import <o:p></o:p></p><p class=MsoPlainText>>> à<o:p></o:p></p><p class=MsoPlainText>>> Bio-Formats" path does something different which works flawless.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I for sure downloaded and installed and use this MATLAB toolbox for <o:p></o:p></p><p class=MsoPlainText>>> using<o:p></o:p></p><p class=MsoPlainText>>> Bio-Formats in MATLAB and believe to have the older LOCI things <o:p></o:p></p><p class=MsoPlainText>>> deleted:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> <a href="http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip"><span style='color:windowtext;text-decoration:none'>http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip</span></a><o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I further believe to remember correctly that I downloaded and <o:p></o:p></p><p class=MsoPlainText>>> installed<o:p></o:p></p><p class=MsoPlainText>>> FiJi, and somehow remember that there was something about ImageJ2 <o:p></o:p></p><p class=MsoPlainText>>> support,<o:p></o:p></p><p class=MsoPlainText>>> which I for sure didn´t reject, whatever it was. If there has been <o:p></o:p></p><p class=MsoPlainText>>> any<o:p></o:p></p><p class=MsoPlainText>>> choice to get FiJi in different versions, then I believe I decided <o:p></o:p></p><p class=MsoPlainText>>> for the<o:p></o:p></p><p class=MsoPlainText>>> FiJi with version ImageJ2 in use. I remember quite well that I <o:p></o:p></p><p class=MsoPlainText>>> decided to<o:p></o:p></p><p class=MsoPlainText>>> not install ImageJ and LOCI plugin anymore but to install for <o:p></o:p></p><p class=MsoPlainText>>> convenience<o:p></o:p></p><p class=MsoPlainText>>> the all-inclusive package FiJi, because I read that then the LOCI<o:p></o:p></p><p class=MsoPlainText>>> bioformats would be integrated, and FiJi update mechanism would also <o:p></o:p></p><p class=MsoPlainText>>> update<o:p></o:p></p><p class=MsoPlainText>>> that bioformats part then.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I am now confused to have seen somewhere on the screen (not sure if <o:p></o:p></p><p class=MsoPlainText>>> it<o:p></o:p></p><p class=MsoPlainText>>> actually was in FiJI or MATLAB), that some SCIFIO is somewhere in use <o:p></o:p></p><p class=MsoPlainText>>> or<o:p></o:p></p><p class=MsoPlainText>>> has been mentioned in a message when opening / importing a dm3 file. <o:p></o:p></p><p class=MsoPlainText>>> I am<o:p></o:p></p><p class=MsoPlainText>>> further confused because I thought to have read somewhere that if the <o:p></o:p></p><p class=MsoPlainText>>> LOCI<o:p></o:p></p><p class=MsoPlainText>>> plugin would be installed that then ImageJ would automatically use <o:p></o:p></p><p class=MsoPlainText>>> it in<o:p></o:p></p><p class=MsoPlainText>>> the standard "File à Open…" path if needed. I am completely <o:p></o:p></p><p class=MsoPlainText>>> confused if I<o:p></o:p></p><p class=MsoPlainText>>> am actually using now the LOCI plugin in ImageJ, or the OME <o:p></o:p></p><p class=MsoPlainText>>> Bio-Formats<o:p></o:p></p><p class=MsoPlainText>>> import filter, or some SciFio thing or whatever, but this should not <o:p></o:p></p><p class=MsoPlainText>>> be the<o:p></o:p></p><p class=MsoPlainText>>> topic here in my bug report.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> In summary: for sure the MATLAB 'bfopen' command does not produce the<o:p></o:p></p><p class=MsoPlainText>>> correct result, and the FiJi "File à Open…" menu neither, but the <o:p></o:p></p><p class=MsoPlainText>>> FiJi<o:p></o:p></p><p class=MsoPlainText>>> "File à Import à Bio-Formats" menu apparently works correctly.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Best greetings from the EM-Labs of CIC biomaGUNE,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Marco Möller<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> ----------------------------------------------------------------<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Marco Möller<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Platform Manager - Electron Microscopy<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> *CIC biomaGUNE*<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Parque Tecnológico de San Sebastián<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Paseo Miramón, 182. Ed. Empresarial C<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> 20009 San Sebastián (Guipúzcoa)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> SPAIN<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Tel: +34 943 00 53 25<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> <a href="mailto:mmoller@cicbiomagune.es"><span style='color:windowtext;text-decoration:none'>mmoller@cicbiomagune.es</span></a><o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> *From:* Balaji Ramalingam [<a href="mailto:b.ramalingam@dundee.ac.uk"><span style='color:windowtext;text-decoration:none'>mailto:b.ramalingam@dundee.ac.uk</span></a>]<o:p></o:p></p><p class=MsoPlainText>>> *Sent:* Tuesday, September 09, 2014 2:54 PM<o:p></o:p></p><p class=MsoPlainText>>> *To:* Marco Moller; <a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style='color:windowtext;text-decoration:none'>ome-devel@lists.openmicroscopy.org.uk</span></a><o:p></o:p></p><p class=MsoPlainText>>> *Subject:* Re: [ome-devel] BIOFORMATS bug report from a user: GATAN <o:p></o:p></p><p class=MsoPlainText>>> dm3<o:p></o:p></p><p class=MsoPlainText>>> not read correctly<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Hi Marco,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Thank you for your detailed summary.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> As suggested, it would be great if you could upload the file to the<o:p></o:p></p><p class=MsoPlainText>>> following URL,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> <a href="https://www.openmicroscopy.org/qa2/qa/upload/"><span style='color:windowtext;text-decoration:none'>https://www.openmicroscopy.org/qa2/qa/upload/</span></a><o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> We will then create a ticket, post investigation and CC you on the <o:p></o:p></p><p class=MsoPlainText>>> same.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Thanks again,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Best,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Balaji<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> __________________<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Mr Balaji Ramalingam<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Software Developer<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> OME Team<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> College of Life Sciences<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> University of Dundee<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> *From: *Marco Moller <<a href="mailto:mmoller@cicbiomagune.es"><span style='color:windowtext;text-decoration:none'>mmoller@cicbiomagune.es</span></a>><o:p></o:p></p><p class=MsoPlainText>>> *Date: *Tuesday, 9 September 2014 08:22<o:p></o:p></p><p class=MsoPlainText>>> *To: *"<a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style='color:windowtext;text-decoration:none'>ome-devel@lists.openmicroscopy.org.uk</span></a>" <<o:p></o:p></p><p class=MsoPlainText>>> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style='color:windowtext;text-decoration:none'>ome-devel@lists.openmicroscopy.org.uk</span></a>><o:p></o:p></p><p class=MsoPlainText>>> *Subject: *[ome-devel] BIOFORMATS bug report from a user: GATAN dm3 <o:p></o:p></p><p class=MsoPlainText>>> not<o:p></o:p></p><p class=MsoPlainText>>> read correctly<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Hello,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I found a bug in the current BIOFORMATS import filter for GATAN *.dm3<o:p></o:p></p><p class=MsoPlainText>>> (Electron Microscopy) files:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> If the original GATAN software stored for a pixel in the image a <o:p></o:p></p><p class=MsoPlainText>>> negative<o:p></o:p></p><p class=MsoPlainText>>> value, then the BIOPFRORMATS import filter does not read this out<o:p></o:p></p><p class=MsoPlainText>>> correctly, but changes the negative value to an extreme high positive <o:p></o:p></p><p class=MsoPlainText>>> value.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I am working with MATLAB and have not much experience with ImageJ, <o:p></o:p></p><p class=MsoPlainText>>> but at<o:p></o:p></p><p class=MsoPlainText>>> least could confirm that this does not only happen with the MATLAB <o:p></o:p></p><p class=MsoPlainText>>> front<o:p></o:p></p><p class=MsoPlainText>>> end ‘bfopen’ of the BIOFORMATS import filter, but also happens <o:p></o:p></p><p class=MsoPlainText>>> when<o:p></o:p></p><p class=MsoPlainText>>> importing such image containing a negative value to ImageJ by the<o:p></o:p></p><p class=MsoPlainText>>> BIOFORMATS import filter used there.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I work on WinXP 32-bit or Win7 64-bit, have FiJi, MATLAB and <o:p></o:p></p><p class=MsoPlainText>>> BIOFORMATS<o:p></o:p></p><p class=MsoPlainText>>> software all in the most up to date version (as of 8 September 2014)<o:p></o:p></p><p class=MsoPlainText>>> installed.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Please have a look on the following little log on querying the max <o:p></o:p></p><p class=MsoPlainText>>> and min<o:p></o:p></p><p class=MsoPlainText>>> pixel value found in the image by different software:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Gatan Digital Micrograph V1.85 (32-bit):<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> GATAN_IMAGE: Minimum -93 at (1920,612)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> GATAN_IMAGE: Maximum 1320 at (2035,135)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Gatan Microscopy Suite Digital Micrograph V2.02.800.0 (32-bit):<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> GATAN_IMAGE: Minimum -93 at (1920,612)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> GATAN_IMAGE: Maximum 1320 at (2035,135)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> MATLAB (64-bit), using BIOFORMATS command ‘bfopen’<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> max = 4294967203 at (613,1921)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> min = 45 at (1722,407)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> after changing manually the (in MATLAB max, in GATAN negative) value <o:p></o:p></p><p class=MsoPlainText>>> to<o:p></o:p></p><p class=MsoPlainText>>> i.e. 1000 using MATLAB command GATAN_IMAGE(613,1921) = 1000, applying<o:p></o:p></p><p class=MsoPlainText>>> ‘bfopen’ in MATLAB shows:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> max: 1320 at (136,2036)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> min: 45 at(1722,407) (which is correct, this I<o:p></o:p></p><p class=MsoPlainText>>> confirmed to before have been the second smallest value in the file)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Checking if this is a ‘bfopen’ behavior or a general BIOFROMATS <o:p></o:p></p><p class=MsoPlainText>>> behavior:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> FiJi (64-bit), using the BIOFORMATS import option:<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> min: 45<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> max: 4,29E+09<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> I would be willing to share the GATAN image file of interest, but <o:p></o:p></p><p class=MsoPlainText>>> prefered<o:p></o:p></p><p class=MsoPlainText>>> not to attach it to the e-mail to the mailing list. If anyone would <o:p></o:p></p><p class=MsoPlainText>>> have<o:p></o:p></p><p class=MsoPlainText>>> interest in the image, please contact me and I can send it then to <o:p></o:p></p><p class=MsoPlainText>>> the<o:p></o:p></p><p class=MsoPlainText>>> interested person(s).<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> As I am meanwhile using the really excellent dm3 import filter <o:p></o:p></p><p class=MsoPlainText>>> written for<o:p></o:p></p><p class=MsoPlainText>>> MATLAB by Andreas Korinek (<o:p></o:p></p><p class=MsoPlainText>>> <a href="http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader"><span style='color:windowtext;text-decoration:none'>http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader</span></a>),<o:p></o:p></p><p class=MsoPlainText>>> which I recommend you to have a look at in order to find much <o:p></o:p></p><p class=MsoPlainText>>> information<o:p></o:p></p><p class=MsoPlainText>>> about the dm3 file structure (much more data is extracted from dm3 <o:p></o:p></p><p class=MsoPlainText>>> than by<o:p></o:p></p><p class=MsoPlainText>>> the present BIOFORMATS filter), my e-mail to the developer list does <o:p></o:p></p><p class=MsoPlainText>>> not<o:p></o:p></p><p class=MsoPlainText>>> ask for your explicit answer. Instead it is cordially meant to just <o:p></o:p></p><p class=MsoPlainText>>> support<o:p></o:p></p><p class=MsoPlainText>>> the BIOFORMATS project by the given information and bug report.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Best greetings from the EM-Labs of CIC biomaGUNE,<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Marco Möller<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> ----------------------------------------------------------------<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Marco Möller<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Platform Manager - Electron Microscopy<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> *CIC biomaGUNE*<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Parque Tecnológico de San Sebastián<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Paseo Miramón, 182. Ed. Empresarial C<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> 20009 San Sebastián (Guipúzcoa)<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> SPAIN<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> Tel: +34 943 00 53 25<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> <a href="mailto:mmoller@cicbiomagune.es"><span style='color:windowtext;text-decoration:none'>mmoller@cicbiomagune.es</span></a><o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> This e-mail is from CIC biomaGUNE. 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Any unauthorised dissemination <o:p></o:p></p><p class=MsoPlainText>>> or<o:p></o:p></p><p class=MsoPlainText>>> copying of this e-mail or its attachments, and any use or disclosure <o:p></o:p></p><p class=MsoPlainText>>> of any<o:p></o:p></p><p class=MsoPlainText>>> information contained in them, is strictly prohibited and may be <o:p></o:p></p><p class=MsoPlainText>>> illegal.<o:p></o:p></p><p class=MsoPlainText>>> If you have received this e-mail in error, please notify or telephone <o:p></o:p></p><p class=MsoPlainText>>> +<o:p></o:p></p><p class=MsoPlainText>>> 34 943 00 53 00 and delete it from your system.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> The University of Dundee is a registered Scottish Charity, No: <o:p></o:p></p><p class=MsoPlainText>>> SC015096<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> This e-mail is from CIC biomaGUNE. The e-mail and any files <o:p></o:p></p><p class=MsoPlainText>>> transmitted<o:p></o:p></p><p class=MsoPlainText>>> with it are confidential and intended solely for the use of the <o:p></o:p></p><p class=MsoPlainText>>> individual<o:p></o:p></p><p class=MsoPlainText>>> or entity to whom they are addressed. Any unauthorised dissemination <o:p></o:p></p><p class=MsoPlainText>>> or<o:p></o:p></p><p class=MsoPlainText>>> copying of this e-mail or its attachments, and any use or disclosure <o:p></o:p></p><p class=MsoPlainText>>> of any<o:p></o:p></p><p class=MsoPlainText>>> information contained in them, is strictly prohibited and may be <o:p></o:p></p><p class=MsoPlainText>>> illegal.<o:p></o:p></p><p class=MsoPlainText>>> If you have received this e-mail in error, please notify or telephone <o:p></o:p></p><p class=MsoPlainText>>> +<o:p></o:p></p><p class=MsoPlainText>>> 34 943 00 53 00 and delete it from your system.<o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>> _______________________________________________<o:p></o:p></p><p class=MsoPlainText>>> ome-devel mailing list<o:p></o:p></p><p class=MsoPlainText>>> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style='color:windowtext;text-decoration:none'>ome-devel@lists.openmicroscopy.org.uk</span></a><o:p></o:p></p><p class=MsoPlainText>>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel"><span style='color:windowtext;text-decoration:none'>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></a><o:p></o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>>><o:p> </o:p></p><p class=MsoPlainText>> _______________________________________________<o:p></o:p></p><p class=MsoPlainText>> ome-devel mailing list<o:p></o:p></p><p class=MsoPlainText>> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style='color:windowtext;text-decoration:none'>ome-devel@lists.openmicroscopy.org.uk</span></a><o:p></o:p></p><p class=MsoPlainText>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel"><span style='color:windowtext;text-decoration:none'>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></a><o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>--<o:p></o:p></p><p class=MsoPlainText>Gregory Jefferis, PhD<o:p></o:p></p><p class=MsoPlainText>Division of Neurobiology<o:p></o:p></p><p class=MsoPlainText>MRC Laboratory of Molecular Biology<o:p></o:p></p><p class=MsoPlainText>Francis Crick Avenue<o:p></o:p></p><p class=MsoPlainText>Cambridge Biomedical Campus<o:p></o:p></p><p class=MsoPlainText>Cambridge, CB2 OQH, UK<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><a href="http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis"><span style='color:windowtext;text-decoration:none'>http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis</span></a><o:p></o:p></p><p class=MsoPlainText><a href="http://jefferislab.org"><span style='color:windowtext;text-decoration:none'>http://jefferislab.org</span></a><o:p></o:p></p><p class=MsoPlainText><a href="http://flybrain.stanford.edu"><span style='color:windowtext;text-decoration:none'>http://flybrain.stanford.edu</span></a><o:p></o:p></p></div><!--[object_id=#cicbiomagune.es#]--><P align=center><FONT size=2><FONT color=#0000ff><FONT face=Arial><SPAN style="FONT-FAMILY: Barmeno; COLOR: teal; FONT-SIZE: 7.5pt; mso-fareast-font-family: 'Times New Roman'; mso-bidi-font-family: Tahoma; mso-ansi-language: EN-GB" lang=EN-GB>This e-mail is from CIC </SPAN><SPAN style="FONT-FAMILY: Barmeno; COLOR: teal; FONT-SIZE: 7.5pt; mso-fareast-font-family: 'Times New Roman'; mso-bidi-font-family: Tahoma; mso-ansi-language: EN-GB; mso-bidi-font-size: 11.0pt" lang=EN-GB>biomaGUNE</SPAN><SPAN style="FONT-FAMILY: Barmeno; COLOR: teal; FONT-SIZE: 7.5pt; mso-fareast-font-family: 'Times New Roman'; mso-bidi-font-family: Tahoma; mso-ansi-language: EN-GB" lang=EN-GB>. 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