Release Note of BV_Analyzer Ver0703

Major changes from Ver0611 are described.

New functions are listed in the following table.

1. The additions in analytical functions - Available for MiCAM ULTIMA / MiCAM02 / MiCAM01 data -

(1-1) Scale on vertical axis of external analog wave

This is the function for changing scale on vertical axis of external analog wave. This allows user to set vertical scale close to inputted real voltage.

* Opening the [Ana Wave Detail Set] window:
Select the [detail] checkbox next to the [Ana] slidebar in the [Control] tab so that the [Set] button can be active. In this situation, push the [Set] button to open the [Ana Wave Detail Set] window.

* Detailed settings for analog waves:
1. Select [V] or [mV] from the [Unit] selectbox.
2. Select the type of imaging system and the range of analog input voltage (only for the MiCAM02) from the [Device] selectbox.
   [+- 1.0V (MC01)] : MiCAM01
   [+- 1.0V (Ultima)] : MiCAM ULTIMA
*Select the range of analog input voltage, depending on the setting of analog input range only in the MiCAM02 processor.
  [+- 1.0V (MC02)] : -1.0V to +1.0V
  [+- 2.5V (MC02)] : -2.5V to +2.5V
  [+- 10V (MC02)] : -10V to +10V
3. Input the number of amplitude applied to analog signal into the [Amplitude] box.
Can change the gain and the offset values for analog wave by adjusting the [Gain]&[Offset]. After adjusting, close this window.

* Analog wave display After setting, the vertical unit for analog wave is displayed. If analog wave is not displayed, unselect the [detail] checkbox.

(1-2) Displaying averaged waveforms on selected lines or selected areas

The functions for displaying averaged waveforms on selected lines or selected areas.

* Opening the [Wave of ROI/Line] window: After selecting a data on the canvas window, select the [View]-[Display Window for Wave of ROI/Line] from the main menu or push the button on the main menu to open the [Wave of ROI/Line] window.

* Magnifying an image Select the magnification for an image from (1). Select the [interpolation] checkbox to magnify an image with the interpolation method. Move the displayed image by adjusting the vertical/horizontal bar if the size of the magnified image is over the upper area.

* Selecting wave number Two lines can be selected in this function. Select wave number from (2). No.1: Red line, No.2: Blue line

* Selecting the area type Select the "line" or the "polygon" from (3).

* Selecting area by drawing line or polygon.
     [Delete] key: Deleting the last point
     [Clear (Select No.)] button: Clearing all lines/area of number selected in (2).
     [No1 -> No2 Copy] button: Copying No.1 lines/area to No.2.
     [No2 -> No1 Copy] button: Copying No.2 lines/area to No.1.
     [Move(Select No.)] button: Moving lines/area of number selected in (2). After pushing this button, drag lines/area on an image to other position.

* Displaying waves Displaying waves by pushing the [Disp Wave] button. Push the this button every time changing lines/area. In the case of polygon, this button doesn't become active until polygon is closed.

* Controlling waves Can adjust the wave gain in the [Gain] slidebar and apply temporal filter to waves in the [Tcnst-Filter] slidebar. Setting on the [Control] tab is applied to wave except the wave gain and the temporal filter.

* Exporting data Can save wave data in a CSV file by pushing the [Save CSV] button. Exported CSV file contains values (=spatially averaged value in a selected area / acquisition averaging times) from frame 0 to the last frame. Note that temporal filter (Tcnst-filter) is also applied to saved values.

(1-3) Median Filter

This function is for removing noise by median filter. The [Median Filter] button was newly added to the [Calculation] tab.

* Processing of this filter is as below.
1. Sort differential value of one pixel and differential values of the nearest 8 pixels by ascending order.
2. Pick up the middle value from sorted 9 values and replace value on one with the new value. The figure below demonstrates the median filter. On the other hand, the current [Spatial Filter] sets an averaged value between 9 pixels to value of central value.

(1-4) First Derivative

* The [DERIV] button is added on the [Calculation] tab. Select the parameter, "3(+/-1)", "7(+/-3)" from the selectbox.

* Algorithm when parameter is 3(+/-1)
If (Point)=(x,y), (frame number)=t and (differential value)=D(x,y,t) ,
       D'(x,y,t) = ( D(x,y,t+1) - D(x,y,t-1) )/2
If t=0,
       D'(x,y,0) = ( (-3)*D(x,y,0) + 4*D(x,y,1) - D(x,y,2) )/2
If t=n-1 (n is the maximum frame number),
       D(x,y,n-1) = ( 3*D(x,y,n-1) - 4*D(x,y,n-2) + D(x,y,n-3) )/2

* Algorithm when parameter is 7(+/-3)

If (Point)=(x,y), (frame number)=t and (differential value)=D(x,y,t) , ("Lagrange function" of 7 points)

       D'(x,y,t) = ( 3*(D(x,y,t+3) - D(x,y,t-3) + 2*( D(x,y,t+2) - D(x,y,t-2) ) + (D(x,y,t+1) - D(x,y,t-1))/28

If t=0 or t=(the maximum frame number), algorithm is the similar to that of parameter=3(+/-1)　

(1-5) User-defined function for spatial filtering

User can build own formula for spatial filtering function.

* Opening the [Calculation of User Function(t)] Push the [User Function(t)] button on the [Calculation] tab.

* Building a function
Input parameters into the "a" to "k" box on the (1) area and push the [Param Set] button. The created function is displayed on the lower area. F(t) means a differential value at frame number=t and F(t-1) is a value at the previous frame and F(t+1) is a value at the next frame.

** Algorithm when t=0 and t=(the maximum frame number) **
In the case that there are no data for calculating like t=0 and t=(the maximum frame number), this software calculates assuming there are the same values at near frames.
In the case of F(t) = ( F(t-1) + F(t) + F(t+1) )/3,
    If t=0,  F(0) = ( F(0) + F(0) + F(1) )/3
    If t=(the maximum frame number),  F(tmax) = (F(tmax-1) + F(tmax) + F(tmax) )/3

* Preview Can move the preview points by dragging the two [Reference Points] on the image. After pushing the [Preview] button in (3), wave calculated with an user-defined function can be displayed on the lower area. An image is not redraw in this case. Push the [Preview] button every time changing preview points and pushing the [Param Set] button.

(ATTN) Wave displayed in this window is NOT applied with spatial filter and temporal filter ([Spc-Filter]>0, [Tcnst-Filter]>1) on the [Control] tab.

* Executing After confirming in the preview, push the [Calculation of User Function] button. This window is closed, and an user-defined function applies to data on the canvas window.

(1-6) Improvement of Activation Map Function

* Display mode can be selected from three types on the [Activation Map Show] window.
  Peak (threshold + maximum amplitude): Displays signal time courses subsequent to maximum intensity signal located within selected frame. The signals are over threshold.
  50% of Vmax-Vmin (threshold + over 50% of maximum amplitude): Displays signal time courses subsequent to 50% intensity signal between maximum and minimum signal within selected frame.  The signals are over threshold.
  NONE (threshold only): Displays signal time courses over threshold

* The figure below is an example when selecting "Peak" and unselecting the [Contour line].

(1-7) Differentiation of data acquired in CDS/FPN mode automatically when loading to BV_Ana

MiCAM ULTIMA data acquired in CDS/FPN mode keeps values of real light intensity, not differential values. This is the function for converting real intensity values to differential values automatically when loading CDS/FPN data to BV_Ana.

* Select the [Auto Reference] checkbox and load data from [File List] by double-clicking data name. This checkbox affects only data acquired with CDS/FPN mode.

* The figures below show CDS data loaded with the [Auto Reference] check on (the upper) and with the [Auto Reference] check off (the lower). With the check on, each value is differential value from frame# 0. With the check off, each value is real light intensity. Therefore values with the check on are larger than those with the check off.

(1-8) Thumbnail display of MiCAM data

* Opening the [BV Thumbnail] Thumbnail display of files in a selected folder. This display can be opened by pushing the [BV Thumbnail] button on the [File List] tab.
This shows lists of background images saved in a selected folder. The maximum number of files shown once in the [BV Thumbnail] are 100 (10x10). If the [BV Thumbnail] is already active, the [BV Thumbnail] window moves to the top window by pushing the [BV Thumbnail] button.

* How to use the BV_Thumbnail
(1) Change folder in the [Folder]-[Open] from the main menu of the [BV Thumbnail].
(2) In order to change data type, select data type in the [Folder]-[Setting of Data Type] from the main menu or push the [All/Unified/Ultima/MC01/Prev02/Deltaron/Tiff] button on the tool bar.
(3) Data information such as data name, frame number, sampling time and averaging time is shown on the lower status bar when moving mouse pointer over each thumbnail.

* Drag and drop data to BV_Ana  Drag thumbnail and drop it on BV_Ana in order to load data easily.

(1-9) Executing BV_Viewer from BV_Ana

* Opening the [BV_Viewer] The [BV Viewer] button is added on the [FileList] tab. The BV Viewer displays not only data information and background image, but also averaged waves on 4 points. If the [BV Viewer] is already active, the [BV Viewer] window displays on the top by pushing the [BV Thumbnail] button.

* How to user the BV Viewer Please refer to this about how to use.

* Drag and drop data to BV_Ana  Drag file name and drop it on BV_Ana in order to load data easily.

(1-10) Conduction velocity vector function

This is for calculating signal conduction velocity from differential values and displaying them as vector.

* Opening the window Select the [View]-[Display Window for Conduction Velocity Vector] from the main menu while data on the canvas window is selected.

0 - 90' : Green
90-180' : Yellow
0 - ( -90') : Blue
(-90) -( -180') : Red

* Algorithms Please refer to this.

* The set of activation time point on the peak, or  on 50% of amplitude of upstroke of the wave
When [Peak] is selected, the peak time point on each pixel is set as the activation time point.  When [50% of Min-Max] is selected, the minimum and maximum values in the set range are detected, and the 50% point is set as Tpk(x, y).

* Zooming of Image
The size of image can be set on 3X, 5X, or 7X.

* Length of vector
[Length] sets the maximum length of vectors on the image.

* Interval of vector
[Space] sets the interval between vectors.  When the number is “1”, vectors on all pixels are displayed.

* Threshold of vector display
[Threshold] may reduce the noise of vectors.  The peak value under the threshold is ignored as “0”.  Be careful that this threshold is connected to [Gain] on [Control] tab page.

* Limitation of conduction velocity
The unit is number of frames.  The unnatural value of the conduction velocity is appears sometimes.  The difference of frame (time point) should be in reasonable range.  This function ignores the conduction velocity which is more than set difference of frames.

* [Export CSV] button exports the frame number (activation time point), the amplitude of the vector and the angle of vector, of all pixels in CSV file format.

* [Export BMP] button　exports the displayed image in BMP format.

(1-11) Others

Fixation of bugs
* can reproduce the [Pixel Ratio Remove] and the [Bleaching] function on the [Calculation] tab when loading ".rmg" file to BV_Ana.
* Takes over status of the [val] checkbox on the [Control] tab when pushing the [Apply All] button.
* There was a bug that BV_Ana aborts when processing the [LPF/HPF] function with analog waves displayed on the canvas window.
* Moved the scale position of vertical line on the [Strip Show] window.
* Regarding MiCAM02 data acquired with SE(time-lapse) mode, changed the time display below an image and vertical scale to real total time including interval time.
* Auto adjustment of image magnification when opening dialog boxes except [Display Window for Wave Size Fix][Display Window for Strip].
* There was a bug when loading color CSV file into activation map.

2. The additionals in acquisition function - Available only for MiCAM02 -

(2-1) New commands for AutoExec function

User can execute automatic sequencer function by editing commands and pushing the [AutoExec] button on the [Acquisition] tab page. Commands for repeating "loop_start","loop_end" and command for waiting "Wait" are added to this function.

* repeat: repeats processes between "loop_start" and "loop_end" for "N times"
    loop_start = N;
            :
    loop_end;

* wait: waits for "N seconds" and doesn't do any process
　　wait=N;　

(Example）
loop_start=4;
acqs;
wait=1;(sec)
loop_end;

4 repetitions of "1 data acquisition and then waiting for 1 seconds"

(2-2) Others

* Inputting some characters into the [Data Name]-[Header] box on the [Acquisition] tab are prohibited. These characters are also prohibited using file name for Microsoft Windows. The number of header characters are limited up to 8.

<Prohibited characters>
"/", "\", "<", ">", "*", "?", """, "|", ":", ";"

* Deleted "Dual-Mirror" from the [Channel] on the [Acquisition] window. Setting for mirror image mode can be done only in  the [Mirror] selectbox on the [Acquisition] tab page.