[ome-users] ZVI opening help

Wed Jun 20 10:52:40 BST 2018

Hi Balaji,
I come back to you with this issue which is still present with your latest version.
Any progress on that?
Thank you for your support
Alban

De : ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] De la part de Balaji Ramalingam (Staff)
Envoyé : jeudi 14 septembre 2017 06:51
À : OME User Support List
Objet : Re: [ome-users] ZVI opening help

Hi,

Thank you for submitting your data.

Having tested it in a variety of different OS/Fiji and Bio-Formats combinations,
we were finally able to reproduce the issue on Windows 10.

This performance issue seems to be windows specific and I have created a card to follow up on that.
https://trello.com/c/rgUGN9Ll/187-zvi-windows-performance-issuefiji

This will get looked into at the earliest.
Thank you again for submitting your data and the plots as requested.

Best,
Balaji

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of "Favre, Alban" <Alban.Favre at ggbearings.com>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Date: Monday, 11 September 2017 at 07:39
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] ZVI opening help

Hi,
The file “mozaicDP4.zvi » is uploaded,
Thank you again for your support .
Regards
Alban

De : ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] De la part de Balaji Ramalingam (Staff)
Envoyé : vendredi 8 septembre 2017 15:46
À : OME User Support List
Objet : Re: [ome-users] ZVI opening help

Hi Alban,

Thank you for sharing the results of the macro.
It clearly looks like the first iteration takes longer than expected.

Unfortunately, we are unable to reproduce the same locally, with the ‘zvi’ files that we have.
Could you please upload the problematic file to the following link?
https://www.openmicroscopy.org/qa2/qa/upload/

This would help us troubleshoot the issue in better detail.

Best,
Balaji

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of "Favre, Alban" <Alban.Favre at ggbearings.com<mailto:Alban.Favre at ggbearings.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Thursday, 7 September 2017 at 14:38
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] ZVI opening help

Hi Balaji,
Sorry for the delay, it’s holiday period in France.
I enclosed the resultant pot, and as you can see the first iteration is quite long.
I used the 5.6 version form 14 august with Fiji 1.51p.
For the moment I simply used the same function as you in my macro code :
run("Bio-Formats Importer", "open=/Users/a_favre/Desktop/mozaicDP4.zvi autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
Thanks in advance
Alban

De : ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] De la part de Balaji Ramalingam (Staff)
Envoyé : vendredi 25 août 2017 18:30
À : OME User Support List
Objet : Re: [ome-users] ZVI opening help

Hi,

Thank you for sharing your issue.
We were unable to reproduce the issue locally with Bio-Formats 5.6.0, Fiji.

I have attached the macro snippet that we used to resolve the time taken over 20 iterations and the resultant plot in this thread,
and we did not see a significant difference in the time taken over the multiple iterations as well.

It would be great if you could please do the following,
1) run the above macro in your Fiji installation (on one of your files which has had issues) and send us a screenshot of the resultant plot
2) Share your macro code as well.

This would help us troubleshoot the issue in better detail.

Best,
Balaji

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of "Favre, Alban" <Alban.Favre at ggbearings.com<mailto:Alban.Favre at ggbearings.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Thursday, 24 August 2017 at 07:33
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] ZVI opening help

Hi,
I am using the bioformat plugin to open ZVI images in a macro.
When I launch it, it takes around 30s just to analyse the image and 2s to really open it.... and half of the time it even do no open anything.
Moreover when its working it open a stack with three different color chanels (c) whereas all the slices are similar.
is there a way to speed up and make more robust  the ZVI opening by preventing stacking or something else?

Thanks in advance!

I am using :

Bioformat 5.6.0

Fiji/imagej 1.51P

below an example of my metadata

BitsPerPixel = 16
_ DimensionOrder = XYCZT_
_ IsInterleaved = true_
_ IsRGB = false_
_ LittleEndian = true_
_ PixelType = uint16_
_ Series 0 Name = RB152.1.2.11F_RB152.1.2.11D.zvi_
_ SizeC = 3_
_ SizeT = 1_
_ SizeX = 11034_
_ SizeY = 15913_
_ SizeZ = 1_
AxioCam Black Reference = false
AxioCam Color Model = true
AxioCam Resolution = 8217
BlackValue = 0.0
Camera = AxioCamICc5
Camera Acquisition Time 0 #1 = 2017-08-23T10:26:50.842
Camera Adapter Magnification = 0.63
Camera Bit Depth = 36
Camera Frame Height = 2056
Camera Frame Width = 2452
Camera Framestart Left = 0
Camera Framestart Top = 0
Camera Shading Correction = true
CameraExposureTimeCalculationControl = 1.0
CameraFrameImageOrientation = 4
CameraFramePixelDistance = 3.45
CameraFrameScalingFactor = 1.0
CameraLiveScalingFactor = 1.0
ContrastManagerMode = 3
Dazzle Protection Active = true
DeviceScalingName = AxioCamICc5
Document Type = Image
Exposure Time [ms] = 12.0
File Date = 1969-12-31T23:59:59.999
Filename = RB152.1.2.11FRB152.1.2.11D.zvi_
Focus Position = 273.45
Focus Position 0 = 273.45
Focus calibrated = false
FocusDepth = 8.8
GammaValue = 0.45
GammaValue 0 = 0.45
Image Channel Index #1 = 0
Image Index S = 0
Image Index T = 0
Image Index Z 0 = 0
Image Memory Usage (RAM) = 1053504316
Image acquisition Index = 0
ImageHeight = 15913
ImageRelativeTime 0 #1 = 0.0 d
ImageRelativeTime1 0 #1 = 0.0 d
ImageRelativeTime2 0 #1 = 0.0 d
ImageRelativeTime3 0 #1 = 0.0 d
ImageRelativeTime4 0 #1 = 0.0 d
ImageTile Index = 0
ImageWidth = 11034
Last modified by = GGBNCYATR
LightManagerEnabled = true
Lightmanager Mode = 2
Location = D:\Resultsmicro\PD276\RB152.1.2.11F_RB152.1.2.11D.zvi_
Microscope Name = Axio Imager.M2
Microscope Port = 5
MicroscopeIllumination = -1
MicroscopeMagnification = 6.3
MicroscopeType = 56
Number Raw Count = 1
NumberOfRawImages = 1
ObjectType = 1
Objective Contrast Method = 2
Objective ID = Objective.422342-9960-000
Objective Immersion Type = 1
Objective Magnification = 10.0
Objective N.A. = 0.25
Objective Name = EC Epiplan-Neofluar 10x/0.25 HD DIC M27
Objective Turret Position = 3
Objective Working Distance = 9000.0
Ocular Total Magnification = 100.0
Original Stage Position X = 23936.187905089406
Original Stage Position X 0 = 23936.187905089406
Original Stage Position Y = -37035.10359353507
Original Stage Position Y 0 = -37035.10359353507
Parfocal Correction = true
PixelType = 8
Reflected Light Aperture = 33.0550918196995
Reflected Light Shutter = 2
ReflectedLightFieldstop = 91.93324061196105
Reflector = Brightfield Refl.light
Reflector ID = Reflector.424928-9901-000
Reflector Position = 1
ReflectorMagnification = 1.0
RelFocusPosition1 0 = 0.0
RelFocusPosition2 0 = 0.0
Scale Factor for X = 1.2226807274950329
Scale Factor for Y = 1.2226807274950329
Scale Factor for Z = 1.0
Scale Height = 19456.51841662846
Scale Unit for X = 76
Scale Unit for Y = 76
Scale Unit for Z = 0
Scale Width = 13491.059147180193
Stage Position X = 30007.16452132049
Stage Position X 0 = 30007.16452132049
Stage Position Y = -27872.242520632724
Stage Position Y 0 = -27872.242520632724
Stage calibrated = false
WhiteValue = 1.0
X position for position #1 = 30007.16452132049
X position for position #2 = 30007.16452132049
Y position for position #1 = -27872.242520632724
Y position for position #2 = -27872.242520632724
tagID_2071 0 = 0.0_
tagID_2298 = 49_
tagID_5510 = 3.0_
tagID_6122 = 2_
tagID_6127 = 4_
tagID_6128 = 7.3390625_
tagID_65666 = 1.0_
tagID_65669 = 0.0_
tagID_65681 = false_

--
(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51p; Java 1.8.066 [64-bit]; Windows 10 10.0; 3250MB of 60000MB (5%)_
_ _
Title: RB152.1.2.11FRB152.1.2.11D.zvi_
Width: 13491.0591 microns (11034)
Height: 19456.5184 microns (15913)
Size: 1005MB
Resolution: 0.8179 pixels per micron
Voxel size: 1.2227x1.2227x1 micron^3
ID: -11
Bits per pixel: 16 (unsigned)
Display ranges
_ 1: 0-65520_
_ 2: 240-65520_
_ 3: 0-65520_
Image: 1/3 (c:1/3 - RB152.1.2.11FRB152.1.2.11D)_
_ Channels: 3_
_ Composite mode: "composite"_
No threshold
Magnification: 0.04
ScaleToFit: false
Uncalibrated
Path: D:\Resultsmicro\PD276\RB152.1.2.11F_RB152.1.2.11D.zvi_
Screen location: 2256,166 (1920x1080)
Coordinate origin: 0,0,0
No overlay
No selection

Alban Favre

R&D Engineer - Product & Process Development

[cid:image001.gif at 01D4088D.30357E10]

GGB France EURL - Annecy

65 Chemin de la Prairie
BP2074

74009 Annecy

France

Tel:

+33450336623

Fax:

Mobil:

E-Mail:

Alban.Favre at ggbearings.com<mailto:Alban.Favre at ggbearings.com>

http://www.ggbearings.com

----------Legal Disclaimer----------

The information contained in this message may be privileged and confidential, and is intended solely for the use of the named addressee. No other person is authorized to access, copy or re-use this message (or any information contained herein). If you are not the intended recipient, please notify us immediately by replying to this message and delete it from your computer.

The University of Dundee is a registered Scottish Charity, No: SC015096

----------Legal Disclaimer----------

The information contained in this message may be privileged and confidential, and is intended solely for the use of the named addressee. No other person is authorized to access, copy or re-use this message (or any information contained herein). If you are not the intended recipient, please notify us immediately by replying to this message and delete it from your computer.

The University of Dundee is a registered Scottish Charity, No: SC015096

----------Legal Disclaimer----------

The information contained in this message may be privileged and confidential, and is intended solely for the use of the named addressee. No other person is authorized to access, copy or re-use this message (or any information contained herein). If you are not the intended recipient, please notify us immediately by replying to this message and delete it from your computer.

The University of Dundee is a registered Scottish Charity, No: SC015096

----------Legal Disclaimer----------

The information contained in this message may be privileged and confidential, and is intended solely for the use of the named addressee. No other person is authorized to access, copy or re-use this message (or any information contained herein). If you are not the intended recipient, please notify us immediately by replying to this message and delete it from your computer.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180620/290c7730/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.gif
Type: image/gif
Size: 18324 bytes
Desc: image001.gif
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180620/290c7730/attachment.gif>