New additional functions of BV_Analyzer
Ver0608
The description of new/modified functions from Ver0602.
The
following list shows new functions.
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1. New analysis functions （for all data formats available） |
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(1-1) |
Differential display without negative value for imaging of heart or
calcium imaging |
This function efficiently displays data
of heart imaging or calcium imaging, which does not have any negative
signal. The reference frames for
each pixel are with maximum or minimum value in set range of timeframe, which
frames are set automatically. |
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(1-2) |
Compensation of the fading (bleaching)
curve in wave display. |
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(1-3) |
BV_Ana can import Muti_image_TIFF (16-bit gray scale) for further analysis. |
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(1-4) |
The set two areas can be extracted as two
data from one data. This function
is for data using fluorescence separator for single camera. |
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(1-5) |
Image axis can be reversed (X or Y), and
also can be rotated. |
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(1-6) |
The set of texts and lines (arrows) on
the canvas can be copied and pasted. |
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(1-7) |
Several texts and lines (arrows) can be
selected, and those attribute can be changed collectively. |
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(1-8) |
Wave data can be exported with % unit in
CSV format. |
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(1-9) |
The display function of the
points over 50% of the amplitude in the set frame range is added to
[Activation Map]. |
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(1-10) |
[Ref Image Substitute] process for
MiCAM02 data was corrected to set pixels of subtracted data onto background
image, accurately. |
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(1-11) |
Other changes. |
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2. New functions for data acquisition
(MiCAM02 only) |
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(2-1) |
Wave preview during
acquisition is available in the acquisition with many averaging times. |
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(2-2) |
Active pixel number of image is
displayed. |
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(2-3) |
Optional Full-size (Acquisition size)
display, which contains input external data. Active pixels image is displayed in
default. |
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(2-4) |
Reflection/rotation modes were added to
acquisition function including single camera mode. |
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1. New analysis functions （for all data formats available）
(1-1) Differential
display without negative value for imaging of heart or calcium imaging
- The appropriate display function for heart
imaging and calcium imaging, which does not have any negative value data.
- [Ref-Min] and [Ref-Max] buttons were added
to [Reference] in [Calculation] page.
- - [Ref-Min] process searches the minimum value about each pixel in the set of
frame range, and recalculates subtracted values, which references are the
searched minimum values. When full
range of data is reprocessed, all value becomes positive.
- -
New values as D’(x, y, z) is calculated according to following formula. D(x, y, z)
shall be the point (x, y) at frame (t), and D(x, y, t_min)
shall be the minimum value in set range.
D'(x,y,t)
= D(x,y,t) - D(x,y,t_min)
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[Ref-Max] process searches the maximum value about each pixel in the set of
frame range, and recalculates subtracted values, which references are the
searched maximum values. When full
range of data is reprocessed, all value becomes negative.
- -
New values as D’(x, y, z) is calculated according to following formula. D(x, y, z)
shall be the point (x, y) at frame (t), and D(x, y, t_min)
shall be the maximum value in set range.
D'(x,y,t)
= D(x,y,t) - D(x,y,t_max)
- [sp] check bottom was added to [Control]
page
- -
When [sp] is checked, the reference value is set onto left-low end of the wave
window. In default setting, the
reference value is on the center of wave window, so that positive/negative
values can be displayed. Check on
[sp] to make it ON after [Ref-Max] process. Check [sp] and [inverse] to make them ON
after [Ref-Min] process.
l
An
example of heart imaging data with [ref-min] process, [sp] and [inverse]
(1-2) [Bleaching] function in [Calculation] page
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This function calibrate of bleaching curve. Select data on the canvas, and click
[Bleaching] bottom in [Remove] of [Calculation] page.
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This is [Bleaching Remove] Box
(1)
Set the positions of four of [Reference Point]
and a [Preview Point] by mouse-dragging, so that waves of each points are
displayed. The gain of waves can be
adjusted using vertical scroll-bar named as [Wave Gain].
(2)
Set the referring frame ranges for the calculation of slope by
mouse-dragging of [Reference Point] shown by blue broken line.
(3)
The width of blue broken line is adjustable by input the number of
frame.
(4)
Click [Preview] button, so that the red wave is displayed after the
calibration with slope between the set two ranges.
(5)
Click [Bleaching Remove] button to process all pixels.
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*** The algorithm of [Bleaching Remove] *** All pixels are processed on
following algorithm. -
The averaged value Vs (x, y)
in the start frame range (frame number: from Fs-n to Fs+n)
is calculated. -
The averaged value Ve (x, y) in the end frame range (frame number: from Fe-n
to Fe+n) is calculated. -
Slope is calculated; S(x,y) = (Ve(x,y) – Vs(x,y))
/ (Fe-Fs) -
Subtracted values of all
frames ( from F0 to Fmax)
are calculated by following formula. D’(x, Y, f) = D(x, y, f) – S(x,y)*f |
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Multi-TIFF data in 16-bit gray-scale can be imported. Each pixel on all frames except the
first frame is subtracted value from the first frame. This function is very useful when data
is transported from or to other software.
Multi-TIFF file also can be exported from BV_Analyzer.
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Click [Movie Export] button after the setting of [start], [end] frames and
[step] in [Time & Movie Control], and [Movie Export] window below appears.
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When [Multi TIFF (16bits-GrayScale)] is checked and click [OK] button,
multi-TIFF including real images is exported. This file can be import into BV_Ana again.
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When [Multi TIFF] is checked and click [OK] button, image data displayed on
canvas is exported in multi-TIFF format.
This file can not be import into BV_Ana again.
(1-4) Data separation; Image extraction
- Two areas in single camera
data can be selected, and can be saved separately. This function can be used for data such
as dual-wavelength imaging using fluorescence splitter onto single CCD
sensor. Separated data can be
applied for other data analysis and processing including overlaid display.
- After data selection, run
[Utility] - [Separate data file] in main menu. [Data separate] window below appears.
(1)
Input pixel size of extracting image. The sizes of two extracted images are
same. The input pixel number should
be a multiple of four, and when the input number is not a multiple of four, the value is changed to the closest number
automatically. The areas for
extraction are shown by red lines.
(2)
Adjust extract areas by mouse-dragging.
(3)
Input file name for extracted data.
(4)
Click [Separate & Save] button.
Two extracted data are saved, and displayed on canvas immediately.
(1-5) Reverse/rotation
of image
- Select data, and click [Reverse &
rotation of image] in the pop up menu which appears by right-click of mouse, or
click 
button in the tool bar.
- After appearance of [Reverse &
rotation of image] window shown as below, select [Horizontal Reverse],
[Vertical Reverse] or [Rotation of 180 degree] and click [OK] for the process.
(1-6) Copy/Paste functions for texts and lines (arrows)
- Texts and lines (arrows) on the canvas
can be copied, and pasted.
- Click texts and/or lines to copy to
clipboard. To select several texts
and/or lines, click target with [Ctrl]-key.
- Run [Edit] – [Copy] in main menu, or
[Copy] in pop-up menu. 
icon in tool bar
is also available.
- To paste the copied texts and/or lines,
run [Edit] – [Paste] in main menu, or click icon in tool bar. When the copied and paste process is
done on same canvas, the pasted appears at lower-right position of the
original. When it is pasted on
different canvas, the pasted appears at same position as original.
(1-7) Collective
attribute change of text / lines (arrows)
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Several texts and/or lines (arrows) can be changed its attribution, and
can be erased at same time.
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Change of texts: Select texts with [Ctrl]-key, if you need to select
more than one text. Select [Modify]
in the right-click pop-up menu.
Then following Box appears.
If you change the text, [include the character string] should be checked
(ON). And input new text. If you
change only font and/or color of text, [include the character string] should be
un-checked (OFF). Then change the font by click [FONT]. Click [OK] to start to change several
texts simultaneously.
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Change lines (arrows): Select lines (arrows) with [Ctrl]-key, if you
need to select more than one line (arrow).
Select [Modify] in the right-click pop-up menu. Then following Box appears. After the change of the setting, click
[OK] to start to change several lines (arrows) simultaneously.
(1-8) Wave data (% unit) in CSV format
- Select [Wave CSV export2 (%)] in pop-up
menu by right-click of mouse, so that wave data in “% unit” can be export. Input new file name into [Save] box, and
click [OK]. All wave data on the
canvas are exported in “% unit”.
The export data covers from zero- to end-frame.
- The exported “% unit” are same as wave
on canvas. So, the wave on canvas
is available even on Microsoft Excel or the other similar software.
- Note: “% unit” here means % of subtracted
value to background value. If data
was not processed by [dF/F] in [Calculation], the %
is based on background values of each pixels. But, if data is processed by [dF/F], % is based on the maximum value of the background.
(1-9) Additional
function for [Activation Map]
- [Activation map] has been able to show
temporal changes of only the regions over the threshold. This version enables to show the regions
where is over 50% of maximum amplitude (V-max50) in the set frame range. The pixels over 50% of maximum amplitude
are searched automatically after the set of frame range manually.
(1-10) Correction of
[Ref Image Substitute]
- [Ref Image Substitute] function can
change background image, so that low-spatial resolution/ high-sensitive data
can be overlaid on the background image at high-spatial resolution. This function in this version was
modified its overlaying process to adjust the pixel position of data and image.
- Some dialog boxes’ sizes are changed, so
that all dialog boxes can be displayed on 1,024 x 768 monitor.
- Canvas can be scrolled by mouse.
- [neg] in
[Control] page was renamed as [inverse]
- The trouble on [movie]-[step] was fixed.
- The last size and position of the window
are reflected to next start up.
- [Display Window for Statistic] shows point information of
[Reference point].
2. New functions for
data acquisition (for MiCAM02
only)
(2-1) Additional
function for preview during data acquisition
- This version can show waves of four points
in the imaging area during averaging data acquisition.
- To show waves, click [show preview2] box
(check mark means “ON”), and then four colored points appears in monitoring
image. Those four points can be
moved by mouse-drag to appropriate position.
- After the click [Acquisition], new box
shown below appears. The box
displays imaging area, the wave of channel-1 of analog input, and the four
waves of four points in the imaging area.
The waves are updated after every acquisition. If acquisition is 4 times averaging,
those waves are updated 4 times after each acquisition.
(2-2) Display of active pixel number
- New [Active Pixels] beside [Size] box in
[Camera Selection] on [Acquisition] page shows the actual active pixel number
for imaging, and the number does not include any pixels for external input
data. The example image below means
that “384 x 256” mode acquires the images at “376 x 252” pixels. The image shown on canvas, and the saved
size of image are also “376 x 252” pixels.
- If [File]-[Data Full Mode] is checked,
full-size data is acquired, displayed and saved.
- The example images below shows the difference of [Data Full Mode] and normal
mode. Upper image shows [Data Full
Mode] display, and lower image shows normal display.
(2-4) Reflection
(Mirror) image mode for single camera
- [Mirror] is added in [Camera Selection]
on [Acquisition] page. [none] makes normal image. [horizontal]
mode changes horizontal axis of image, [vertical] mode changes vertical axis of
image, and [rotate of 180] rotates image 180-degrees.
- If [Channel] is [camera1] or [camera2],
and [Mirror] is not [none], the inverted-image or
rotated-image from single camera is displayed on the monitor, and saved.
- If [Cannel] is [dual], and [Mirror] is
not [none], only the image from Camera-2 is inverted
or rotated, displayed on the monitor, and saved.
