Here I have created this circiut for building CCD spectrometer. I am using TCD1304AP CCD and Ardiuno Mega. I have written this below code.
<

#include <util/delay.h>

#ifdef ARDUINO_AVR_MEGA2560
#define LAMP 0x20
#define SH 0x40
#define ICG 0x80
#define MCLK 0x10
#else
#define LAMP 0x01
#define SH 0x02
#define ICG 0x04
#define MCLK 0x08
#endif

#define CLOCK PORTB
#define MIN_SIGNAL 10

uint16_t buffer[800];
uint16_t avg = 0;
char cmdBuffer[16];
int cmdIndex;
int exposureTime = 20;

void setup() {
    // Initialize the clocks.
    DDRB |= (LAMP | SH | ICG | MCLK); // Set the clock lines to outputs
    CLOCK |= ICG; // Set the integration clear gate high.

    // Enable the serial port.
    Serial.begin(115200);

    // Setup timer2 to generate a 380.614kHz frequency on D11
    TCCR2A = +(0 << COM2A1) | (1 << COM2A0) | (1 << WGM21) | (0 << WGM20);
    TCCR2B = (0 << WGM22) | (1 << CS20);
    OCR2A = 20;
    TCNT2 = 1;

    // Set the ADC clock to sysclk/32
    ADCSRA &= ~((1 << ADPS2) | (1 << ADPS1) | (1 << ADPS0));
    ADCSRA |= (1 << ADPS2) | (1 << ADPS0);
}

void readCCD(void) {
    int x;
    uint16_t result;

    CLOCK &= ~ICG;
    _delay_loop_1(12);
    CLOCK |= SH;
    delayMicroseconds(5);
    CLOCK &= ~SH;
    delayMicroseconds(15);
    CLOCK |= ICG;
    delayMicroseconds(1);

    for (x = 0; x < 800; x++) {
        CLOCK |= SH;

        if (x == 0) {
            result = (uint16_t)(1023 - analogRead(A0));
            if (result > MIN_SIGNAL) {
                avg = result - MIN_SIGNAL;
            } else {
                avg = result;
            }
        } else {
            result = (uint16_t)(1023 - analogRead(A0));
        }
        CLOCK &= ~SH;
        if (result < avg) {
            result = 0;
        } else {
            result -= avg;
        }
        buffer[x] = result;
        delayMicroseconds(20);
    }
}

void sendData(void) {
    int x;

    for (x = 0; x < 800; ++x) {
        Serial.println(buffer[x]);
    }
}

void loop() {
    while (Serial.available()) {
        cmdBuffer[cmdIndex++] = Serial.read();
    }
    if (cmdBuffer[0] == 'r') {
        sendData();
    } else if (cmdBuffer[0] == 'l') {
        CLOCK &= ~LAMP;
    } else if (cmdBuffer[0] == 'L') {
        CLOCK |= LAMP;
    } else if (cmdBuffer[0] == 'e') {
        exposureTime = atoi((char *)&cmdBuffer[1]);
        if (exposureTime > 1000) exposureTime = 1000;
        else if (exposureTime < 0) exposureTime = 0;
        Serial.println(exposureTime);
    }
    memset(cmdBuffer, 0 , sizeof(cmdBuffer));
    cmdIndex = 0;
    readCCD();
    delay(exposureTime);
}

After running this code, we are not able to get required output. Help

 

If you go through that code listing line by line and understand what each line does, it will become rather obvious what the failure is.
Aside from that, an arduino is not suitable for such an application.