[ome-devel] BIOFORMATS bug report from a user: GATAN dm3 not read correctly

Tue Sep 9 20:00:20 BST 2014

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
[2] https://github.com/fiji/IO/blob/master/src/main/java/io/DM3_Reader.java

On Tue, Sep 9, 2014 at 11:46 AM, Marco Moller <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
>
>
>
> 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
>
>
>
> *From:* Balaji Ramalingam [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
> *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/
>
>
>
> 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>
> *Date: *Tuesday, 9 September 2014 08:22
> *To: *"ome-devel at lists.openmicroscopy.org.uk" <
> 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),
> 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
>
>
>
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