If you have already seen the digital thermometer schematic then by using same circuit diagram you will be able to make your own counter

The Program for the counter is given below while the circuit diagram is same as Digital thermometer without LM35 and 3rd display
#include <avr/io.h>
#include <avr/interrupt.h>
#include <util/delay_basic.h>


#define SEVEN_SEGMENT_PORT PORTD
#define SEVEN_SEGMENT_DDR DDRD

volatile unsigned char digits[2];


void SevenSegment(unsigned char n)
{
/*
This function writes a digits given by n to the display

Note:
n must be less than 9
*/
 if(n<10)
 {
  switch (n)
  {
  case 0:
  SEVEN_SEGMENT_PORT=0x3f;
  break;

  case 1:
  SEVEN_SEGMENT_PORT=0x0c;
  break;

  case 2:
  SEVEN_SEGMENT_PORT=0x5b;
  break;

  case 3:
  SEVEN_SEGMENT_PORT=0x5e;
  break;

  case 4:
  SEVEN_SEGMENT_PORT=0x6c;
  break;

  case 5:
  SEVEN_SEGMENT_PORT=0x76;
  break;

  case 6:
  SEVEN_SEGMENT_PORT=0x77;
  break;

  case 7:
  SEVEN_SEGMENT_PORT=0x1c;
  break;

  case 8:
  SEVEN_SEGMENT_PORT=0x7f;
  break;

  case 9:
  SEVEN_SEGMENT_PORT=0x7e;
  break;
  }
  }
} 

void Wait() // this loop is responsible for the counting time
{
 unsigned char i;
 for(i=0;i<4;i++) // changing the value of i change the counting speed
 {
  _delay_loop_2(0);
 }
}

void Print(unsigned int num)
{
 /*
 
 This function breaks apart a given integer into separete digits
 and writes them to the display array i.e. digits[]
 
 */
 unsigned char i=0;
 unsigned char j;
 if(num>99) return;


 while(num)
 {
  digits[i]=num%10;
  i++;

  num=num/10;
 }
 for(j=i;j<2;j++) digits[j]=0;
}
 
 
void main()
{
 unsigned int i;

 // Prescaler = FCPU/8 it led to the speed of switching of the display
 TCCR0|=(1<<CS01);

 //Enable Overflow Interrupt Enable
 TIMSK|=(1<<TOIE0);

 //Initialize Counter
 TCNT0=0;

 //Port B[1,0] as out put
 DDRB|=0b00000011;
 PORTB=0b00000000;

 //Port D
 SEVEN_SEGMENT_DDR=0XFF;

 //Turn off all segments
 SEVEN_SEGMENT_PORT=0XFF;

 //Enable Global Interrupts
 sei();

 //Infinite loop
 //Print a number from 1 to 99
 while(1)
 {
  for(i=0;i<100;i++)
  {
  Print(i);
  Wait();
  }

 }
}

ISR(TIMER0_OVF_vect)
{
 /*

 This interrup service routine (ISR)
 Updates the displays

 */
 static unsigned char i=0;

 if(i==1)
 {
  //If on last display then come
  //back to first.
  i=0;
 }
 else
 {
  //Goto Next display
  i++;
 }

 //Acivate a display according to i
 PORTB=~(1<<i);

 //Write the digit[i] in the ith display.
 SevenSegment(digits[!i]); // I do the complement of i as i have connected the PB1 AND PB0 in opposite way

}
################
/*

Description:   Program to demonstrate the use of Seven

            Segment Displays In Multiplexed Mode.
________________________________________________________

Author:  Avinash Gupta
Date: 11 Oct 08
Web      www.eXtremeElectronics.co.in

  
*/

#include <avr/io.h>
#include <avr/interrupt.h>
#include <util/delay_basic.h>


#define SEVEN_SEGMENT_PORT PORTD
#define SEVEN_SEGMENT_DDR DDRD

volatile uint8_t digits[3];


void SevenSegment(uint8_t n,uint8_t dp)
{
/*
This function writes a digits given by n to the display
the decimal point is displayed if dp=1

Note:

n must be less than 9
*/
   if(n<10)
   {
      switch (n)
      {
         case 0:
         SEVEN_SEGMENT_PORT=0b00000011;
         break;

         case 1:
         SEVEN_SEGMENT_PORT=0b10011111;
         break;

         case 2:
         SEVEN_SEGMENT_PORT=0b00100101;
         break;

         case 3:
         SEVEN_SEGMENT_PORT=0b00001101;
         break;

         case 4:
         SEVEN_SEGMENT_PORT=0b10011001;
         break;

         case 5:
         SEVEN_SEGMENT_PORT=0b01001001;
         break;

         case 6:
         SEVEN_SEGMENT_PORT=0b01000001;
         break;

         case 7:
         SEVEN_SEGMENT_PORT=0b00011111;
         break;

         case 8:
         SEVEN_SEGMENT_PORT=0b00000001;
         break;

         case 9:
         SEVEN_SEGMENT_PORT=0b00001001;
         break;
      }
      if(dp)
      {
         //if decimal point should be displayed

         //make 0th bit Low
         SEVEN_SEGMENT_PORT&=0b11111110;
      }
   }
   else
   {
      //This symbol on display tells that n was greater than 9
      //so display can't handle it

      SEVEN_SEGMENT_PORT=0b11111101;
   }
}

void Wait()
{
   uint8_t i;
   for(i=0;i<10;i++)
   {
      _delay_loop_2(0);
   }
}

void Print(uint16_t num)
{
   /*

  
   This function breaks apart a given integer into separete digits
   and writes them to the display array i.e. digits[]
  
   */
   uint8_t i=0;
   uint8_t j;
   if(num>999) return;


   while(num)
   {
      digits[i]=num%10;
      i++;

      num=num/10;
   }
   for(j=i;j<3;j++) digits[j]=0;
}





void main()
{
   uint16_t i;

   // Prescaler = FCPU/1024
   TCCR0|=(1<<CS02);

   //Enable Overflow Interrupt Enable
   TIMSK|=(1<<TOIE0);

   //Initialize Counter

   TCNT0=0;

   //Port B[2,1,0] as out put
   DDRB|=0b00000111;

   PORTB=0b00000110;

   //Port D
   SEVEN_SEGMENT_DDR=0XFF;

   //Turn off all segments

   SEVEN_SEGMENT_PORT=0XFF;

   //Enable Global Interrupts
   sei();

   //Infinite loop
   //Print a number from 1 to 999
   while(1)
   {
      for(i=0;i<1000;i++)
      {
         Print(i);
         Wait();
      }

   }
}

ISR(TIMER0_OVF_vect)
{
   /*

   This interrup service routine (ISR)
   Updates the displays

   */
   static uint8_t i=0;

   if(i==2)
   {
      //If on last display then come

      //back to first.
      i=0;
   }
   else
   {
      //Goto Next display
      i++;
   }

   //Acivate a display according to i

   PORTB=~(1<<i);

   //Write the digit[i] in the ith display.
   SevenSegment(digits[i],0);

}

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