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

[Balaji Ramalingam]

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<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), 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

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mmoller at cicbiomagune.es<mailto:mmoller at cicbiomagune.es>


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