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  NeuroPlex

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Description: Propagating population signal from the turtle visual cortex. Provided by Jim Prechtl, Larry Cohen and David Kleinfeld, Yale University and UCSD.

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NeuroPlex Data File Structures

Header

The size of the header is 5120 bytes (2560 integers).
All values described are signed 16 bit integers.
The following is important information needed for data analysis and display.

Photodiode array (NeuroPDA and NeuroPDA-II):

Number of Frames

5th Integer

Number of Pixels

97th Integer

Frame Interval (msec per frame)

(Number of Pixels*4th Integer)/20000.0

Resting Light Intensities (RLIs)

Starting at the 385th Integer

Map

See below (in the format of IDL code)

 

 

The following piece of code will be helpful for displaying the output on a "Page Display":

PRO H464_fill, diode_ar             ;map for WuTech Hexagon 464 -- diode_ar
diode_ar=INTARR(25,25)
diode_ar=[[  0,  0,  0,  0,  0,  0,  0,237,236,235,234,233,  7,  6,  5,  4,  3,  2,  1,  0,  0,  0,  0,  0,  0], $
          [  0,  0,  0,  0,  0,244,243,242,241,240,239,238, 14, 13, 12, 11, 10,  9,  8,  0,  0,  0,  0,  0,  0], $
          [465,466,467,468,  0,252,251,250,249,248,247,246,245, 21, 20, 19, 18, 17, 16, 15,  0,469,470,471,472], $
          [  0,  0,  0,  0,260,259,258,257,256,255,254,253, 29, 28, 27, 26, 25, 24, 23, 22,  0,  0,  0,  0,  0], $
          [  0,  0,  0,  0,268,267,266,265,264,263,262,261, 38, 37, 36, 35, 34, 33, 32, 31, 30,  0,  0,  0,  0], $
          [  0,  0,  0,277,276,275,274,273,272,271,270,269, 47, 46, 45, 44, 43, 42, 41, 40, 39,  0,  0,  0,  0], $
          [  0,  0,  0,287,286,285,284,283,282,281,280,279,278, 56, 55, 54, 53, 52, 51, 50, 49, 48,  0,  0,  0], $
          [  0,  0,297,296,295,294,293,292,291,290,289,288, 66, 65, 64, 63, 62, 61, 60, 59, 58, 57,  0,  0,  0], $
          [  0,  0,307,306,305,304,303,302,301,300,299,298, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67,  0,  0], $
          [  0,318,317,316,315,314,313,312,311,310,309,308, 88, 87, 86, 85, 84, 83, 82, 81, 80, 79, 78,  0,  0], $
          [  0,330,329,328,327,326,325,324,323,322,321,320,319, 99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 89,  0], $
          [342,341,340,339,338,337,336,335,334,333,332,331,111,110,109,108,107,106,105,104,103,102,101,100,  0], $
          [  0,353,352,351,350,349,348,347,346,345,344,343,123,122,121,120,119,118,117,116,115,114,113,112,  0], $
          [365,364,363,362,361,360,359,358,357,356,355,354,135,134,133,132,131,130,129,128,127,126,125,124,  0], $
          [  0,377,376,375,374,373,372,371,370,369,368,367,366,146,145,144,143,142,141,140,139,138,137,136,  0], $
          [  0,388,387,386,385,384,383,382,381,380,379,378,157,156,155,154,153,152,151,150,149,148,147,  0,  0], $
          [  0,  0,398,397,396,395,394,393,392,391,390,389,168,167,166,165,164,163,162,161,160,159,158,  0,  0], $
          [  0,  0,408,407,406,405,404,403,402,401,400,399,178,177,176,175,174,173,172,171,170,169,  0,  0,  0], $
          [  0,  0,  0,418,417,416,415,414,413,412,411,410,409,187,186,185,184,183,182,181,180,179,  0,  0,  0], $
          [  0,  0,  0,427,426,425,424,423,422,421,420,419,196,195,194,193,192,191,190,189,188,  0,  0,  0,  0], $
          [  0,  0,  0,  0,435,434,433,432,431,430,429,428,205,204,203,202,201,200,199,198,197,  0,  0,  0,  0], $
          [  0,  0,  0,  0,443,442,441,440,439,438,437,436,213,212,211,210,209,208,207,206,  0,  0,  0,  0,  0], $
          [  0,  0,  0,  0,  0,451,450,449,448,447,446,445,444,220,219,218,217,216,215,214,  0,  0,  0,  0,  0], $
          [  0,  0,  0,  0,  0,458,457,456,455,454,453,452,227,226,225,224,223,222,221,  0,  0,  0,  0,  0,  0], $
          [  0,  0,  0,  0,  0,  0,  0,464,463,462,461,460,459,232,231,230,229,228,  0,  0,  0,  0,  0,  0,  0]]
END

 

CCD/CMOS cameras :

Number of Frames

5th Integer

Number of Columns

385th Integer

Number of Rows

386th Integer

Frame Interval (msec per frame)

389th Integer/1000.0
** Dividing Factor = 391st Integer
** If Frame Interval>=10, Then Frame Interval = Frame Interval*Dividing Factor

Acquisition Ratio (electrical over optical)

392nd Integer
** IF Acquisition Ratio=0, Then Acquisition Ratio = 1

Resting Light Intensities (RLIs)

A frame of offset taken in the dark before shutter opening is stored at the end of the file after data. In NeuroPlex software, the RLI of NeuroCCD is obtained by averaging 6th to 11th data frames and subtracting the offset.

Map

Row after row, sequential; e.g. for a 80x80 camera, it is:

1

2

3

...

80

81

82

83

...

160

...





...





6321

6322

6323

...

6400

For the CMOS-DW128 cameras there will be 128 rows of 128 pixels (up to #16384). 

Dual head CCD/CMOS systems: 
All parameters in the header are the same as for the single camera and the program will calculate the RLIs from the same frames as above. The map organization is different :  
 MapThe system views the data as if it is from one 160x80 chip. The data is arranged row after row, sequentially in the following way :

1

2

3

...

160

81

82

83

...

320

...





...





6321

6322

6323

...

12800

and each row contains data from both heads.
For the Dual head CMOS system, each chip is read as 80X128 pixels (rather than the full chip -  128X128 ). Thus the total number of pixels is #160X128 = 20480 organized in rows of 160 data points each.

 

Data

Starting after 5120 bytes (2560 integers) of header info, the data is arranged trace by trace (not frame by frame). The sequence of the traces is from Pixel 1 through Pixel M sequentially.
Point 1, Point 2, ... Point N, (Pixel 1)
Point 1, Point 2, ... Point N, (Pixel 2)
...
...
...
Point 1, Point 2, ... Point N, (Pixel M)
where M = 464 for NeuroPDA, M = 6400 for NeuroCCD (unbinned), M = 65536 for the NeuroCCD-SM256, and M=16384 for the CMOS cameras.
The BNC data is stored following the optical data: (Note: The program records all 8 BNC channels independent of the number of channels used)
Point 1, Point 2, ... Point N*BNC_ratio, (BNC 1)
...
...
Point 1, Point 2, ... Point N*BNC_ratio, (BNC 8)
For the CCD-SMQ, CCD-SM256 and the CMOS-DW128 the dark frame is stored last : Dark Frame (number of rows * number of columns + 8)
In  a case where the available RAM is small compared to the amount of data in a file, the program uses a different format where the data is organized Frame-by-Frame (rather than Trace-by-Trace). When reading back this type of data file, NeuroPlex asks you to select a section of data to read. The BNC data is attached behind the the optical data and the dark frame stored last (as above).
If you used Write Directly to Disk for acquisition, the arrangement of the data, after the header, is Frame-by-Frame, rather than Trace-by-Trace. The first few frames are "dark" frames (before the shutter opening.) Neuroplex uses the 3rd frame to calculate the total light, but if you are writing your own software, you might check how many "dark" frames are there and average all or part of them. The BNC data is attached after the camera data. In addition, each frame needs to be de-interleaved. Please email us to obtain the pixel map