Bioformat: speed up ZVI images opening

bio-formats
Tags: #<Tag:0x00007fd548768778>

#1

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…
Moreover it open each time a stack with three different color chanels © whereas all the slices are similar.
is there a way to speed up the ZVI opening by preventing stacking or something else?
Thnanks in advance!

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 = RB152.1.2.11F_RB152.1.2.11D.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:\Results_micro\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
tag_ID_2071 0 = 0.0
tag_ID_2298 = 49
tag_ID_5510 = 3.0
tag_ID_6122 = 2
tag_ID_6127 = 4
tag_ID_6128 = 7.3390625
tag_ID_65666 = 1.0
tag_ID_65669 = 0.0
tag_ID_65681 = false

------------------------------------------------------
(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51p; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 3250MB of 60000MB (5%)
 
Title: RB152.1.2.11F_RB152.1.2.11D.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 - RB152.1.2.11F_RB152.1.2.11D)
  Channels: 3
  Composite mode: "composite"
No threshold
Magnification: 0.04
ScaleToFit: false
Uncalibrated
Path: D:\Results_micro\PD276\RB152.1.2.11F_RB152.1.2.11D.zvi
Screen location: 2256,166 (1920x1080)
Coordinate origin:  0,0,0
No overlay
No selection

#2

Dear @kalaksas,

to speed up the process, contact the Bio-Formats team directly and raise awareness of this issue. They are reading this forum as well, but response times are faster on the channels described in the link.

Best,
Stefan