[ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly
Marco Moller
mmoller at cicbiomagune.es
Thu Sep 11 09:47:17 BST 2014
Dear Greg, Dear Curtis,
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.
Well, now I found more information, following your guidance in your comments:
> 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.
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.
The error occurs in MATLAB (2014a) using 'bfopen' from this package:
http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip
By the way,
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;" .
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:
"
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/C:/Program%20Files/MATLAB/R2014a/java/jarext/slf4j/slf4j-log4j12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Program%20Files/BIOFORMATS/bioformats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
"
This SLF4J error message does not appear if using the dynamic binding.
Some tiny part of the full information about this SLF43J error given on the mentioned SLF4J website :
"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."
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.
Best greetings from the EM-Labs of CIC biomaGUNE,
Marco
-----Original Message-----
From: Dr Gregory Jefferis [mailto:jefferis at mrc-lmb.cam.ac.uk]
Sent: Wednesday, September 10, 2014 11:17 PM
To: Marco Moller
Cc: OME-devel mailing list; Curtis Rueden
Subject: Re: [ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly
Dear Marco,
Given Curtis' point below, it would be to check that this is not in the
DM3 reader bundled with Fiji (which I wrote).
http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html <http://rsb.info.nih.gov/ij/plugins/DM3_Reader.html>
If you send me your file, I can check.
Best wishes,
Greg Jefferis.
On 9 Sep 2014, at 20:00, Curtis Rueden wrote:
> Hi Marco,
>
>> Apparently, the FiJi "File > Open…" path uses some identical step as
>> the MATLAB /Bio-Formats command 'bfopen' does, while the "File >
>> Import > Bio-Formats" path does something different which works
>> flawless.
>
> There are several different scenarios:
>
> 1) Fiji's File > Open with SCIFIO disabled [1]
> 2) Fiji's File > Open with SCIFIO enabled
> 3) File > Import > Bio-Formats
> 4) The MATLAB bfopen script
>
> In case (1), Fiji will use a bundled DM3 reader plugin [2], which
> takes precedence over Bio-Formats.
>
> In cases (2), (3) and (4), Bio-Formats will be used.
>
> Regards,
> Curtis
>
> [1] http://imagej.net/SCIFIO <http://imagej.net/SCIFIO>
> [2]
> https://github.com/fiji/IO/blob/master/src/main/java/io/DM3_Reader.jav <https://github.com/fiji/IO/blob/master/src/main/java/io/DM3_Reader.jav>
> a
>
> On Tue, Sep 9, 2014 at 11:46 AM, Marco Moller
> <mmoller at cicbiomagune.es <mailto:mmoller at cicbiomagune.es> >
> wrote:
>
>> Hello,
>>
>> 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).
>>
>>
>>
>> Let me take the chance and add some further, important observations I
>> did
>> today:
>>
>> 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:
>>
>> File à Import à Bio-Formats
>>
>> 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.
>>
>>
>>
>> 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’:
>>
>> File à Open…
>>
>> does not work correctly.
>>
>>
>>
>> Apparently, the FiJi "File à Open…" path uses some identical step
>> as the
>> MATLAB /Bio-Formats command 'bfopen' does, while the "File à Import
>> à
>> Bio-Formats" path does something different which works flawless.
>>
>>
>>
>>
>>
>>
>>
>> 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:
>>
>>
>> http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip <http://downloads.openmicroscopy.org/bio-formats/5.0.4/artifacts/bfmatlab.zip>
>>
>>
>>
>> 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.
>>
>>
>>
>> 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 à 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.
>>
>>
>>
>> In summary: for sure the MATLAB 'bfopen' command does not produce the
>> correct result, and the FiJi "File à Open…" menu neither, but the
>> FiJi
>> "File à Import à Bio-Formats" menu apparently works correctly.
>>
>>
>>
>>
>>
>>
>>
>> Best greetings from the EM-Labs of CIC biomaGUNE,
>>
>> Marco Möller
>>
>>
>>
>>
>>
>>
>>
>> ----------------------------------------------------------------
>>
>> Marco Möller
>>
>> Platform Manager - Electron Microscopy
>>
>>
>>
>> *CIC biomaGUNE*
>>
>> Parque Tecnológico de San Sebastián
>>
>> Paseo Miramón, 182. Ed. Empresarial C
>>
>> 20009 San Sebastián (Guipúzcoa)
>>
>> SPAIN
>>
>>
>>
>> Tel: +34 943 00 53 25
>>
>> mmoller at cicbiomagune.es <mailto:mmoller at cicbiomagune.es>
>>
>>
>>
>> *From:* Balaji Ramalingam [mailto:b.ramalingam at dundee.ac.uk <mailto:b.ramalingam at dundee.ac.uk> ]
>> *Sent:* Tuesday, September 09, 2014 2:54 PM
>> *To:* Marco Moller; ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
>> *Subject:* Re: [ome-devel] BIOFORMATS bug report from a user: GATAN
>> dm3
>> not read correctly
>>
>>
>>
>> Hi Marco,
>>
>>
>>
>> Thank you for your detailed summary.
>>
>> As suggested, it would be great if you could upload the file to the
>> following URL,
>>
>>
>>
>> https://www.openmicroscopy.org/qa2/qa/upload/ <https://www.openmicroscopy.org/qa2/qa/upload/>
>>
>>
>>
>> We will then create a ticket, post investigation and CC you on the
>> same.
>>
>>
>>
>> Thanks again,
>>
>>
>>
>> Best,
>>
>> Balaji
>>
>>
>>
>> __________________
>>
>> Mr Balaji Ramalingam
>>
>> Software Developer
>>
>> OME Team
>>
>> College of Life Sciences
>>
>> University of Dundee
>>
>>
>>
>> *From: *Marco Moller <mmoller at cicbiomagune.es <mailto:mmoller at cicbiomagune.es> >
>> *Date: *Tuesday, 9 September 2014 08:22
>> *To: *"ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk> " <
>> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk> >
>> *Subject: *[ome-devel] BIOFORMATS bug report from a user: GATAN dm3
>> not
>> read correctly
>>
>>
>>
>> Hello,
>>
>> I found a bug in the current BIOFORMATS import filter for GATAN *.dm3
>> (Electron Microscopy) files:
>>
>> 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.
>>
>> 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.
>>
>> 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.
>>
>>
>>
>> Please have a look on the following little log on querying the max
>> and min
>> pixel value found in the image by different software:
>>
>>
>>
>> Gatan Digital Micrograph V1.85 (32-bit):
>>
>> GATAN_IMAGE: Minimum -93 at (1920,612)
>>
>> GATAN_IMAGE: Maximum 1320 at (2035,135)
>>
>>
>>
>> Gatan Microscopy Suite Digital Micrograph V2.02.800.0 (32-bit):
>>
>> GATAN_IMAGE: Minimum -93 at (1920,612)
>>
>> GATAN_IMAGE: Maximum 1320 at (2035,135)
>>
>>
>>
>> MATLAB (64-bit), using BIOFORMATS command ‘bfopen’
>>
>> max = 4294967203 at (613,1921)
>>
>> min = 45 at (1722,407)
>>
>> 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:
>>
>> max: 1320 at (136,2036)
>>
>> min: 45 at(1722,407) (which is correct, this I
>> confirmed to before have been the second smallest value in the file)
>>
>>
>>
>> Checking if this is a ‘bfopen’ behavior or a general BIOFROMATS
>> behavior:
>>
>> FiJi (64-bit), using the BIOFORMATS import option:
>>
>> min: 45
>>
>> max: 4,29E+09
>>
>>
>>
>> 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).
>>
>>
>>
>> As I am meanwhile using the really excellent dm3 import filter
>> written for
>> MATLAB by Andreas Korinek (
>> http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader <http://www.mathworks.de/matlabcentral/fileexchange/45933-gatan-digital-micrograph-file-reader> ),
>> 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.
>>
>> Best greetings from the EM-Labs of CIC biomaGUNE,
>>
>> Marco Möller
>>
>>
>>
>>
>>
>>
>>
>> ----------------------------------------------------------------
>>
>> Marco Möller
>>
>> Platform Manager - Electron Microscopy
>>
>>
>>
>> *CIC biomaGUNE*
>>
>> Parque Tecnológico de San Sebastián
>>
>> Paseo Miramón, 182. Ed. Empresarial C
>>
>> 20009 San Sebastián (Guipúzcoa)
>>
>> SPAIN
>>
>>
>>
>> Tel: +34 943 00 53 25
>>
>> mmoller at cicbiomagune.es <mailto:mmoller at cicbiomagune.es>
>>
>>
>>
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--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis <http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis>
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This e-mail is from CIC biomaGUNE. The e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this e-mail or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this e-mail in error, please notify or telephone + 34 943 00 53 00 and delete it from your system.
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