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

Thu Sep 11 07:52:12 BST 2014

Dear Greg,
Please find attached the dm3 file containing a negative pixel value -93 at position (1920,612).
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

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
> [2]
> 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>
> 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
>>
>>
>>
>> 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.
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: 
>> SC015096
>>
>> 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.
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

--
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://jefferislab.org
http://flybrain.stanford.edu
-------------- next part --------------
A non-text attachment was scrubbed...
Name: GATAN_IMAGE.zip
Type: application/x-zip-compressed
Size: 6041033 bytes
Desc: GATAN_IMAGE.zip
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20140911/2aeaf3f0/attachment-0001.bin>