OpenHolter project: D.I.Y. Electrocardiography using Arduino and Django

Transcript

1. The OpenHolter Project: D.I.Y. Cardiometry with Arduino and Django. Roberto

   Rosario robertorosario.com

2. Who am I?

3. Who am I? Hint: Not him.

4. Who am I?

5. Who am I?

6. Who am I?

7. DISCLAIMER I’m not a doctor or a medical practitioner. This

   talk is about my personal experiences and covers my basic understanding about some topics using Internet sources. I share this as an introduction of these topics only. This talk is not meant to be a scientifically accurate document, do not use it or reference it as such. There many things in this talk that can be and should have been made differently/better. The device shown in this talk is not meant or claims to diagnose or cure heart diseases or conditions. I’m not endorsing that you build this device. The material in this talk doesn’t substitute a visit to your doctor or the years of study they endure to become doctors or the years of experience they endure to become experts. If you decide use the information shown in this talk or build the device shown in this talk, you do so at your own risk and assume any and all consequences of such decision, relieving me of any and all liabilities.

8. What is Cardiometry? Cardio = Heart Metry = Measurement

9. What is Electro Cardiometry? Electro = Electricity Cardio = Heart

   Metry = Measurement

10. What is an EKG (or ECG) Acronym: Electro Cardio Gram

    Electric Heart Diagram

11. Sample EKG. Wikipedia, Public Domain

12. Cardiac pacemaker. Wikipedia, CC BY-SA 2.5

13. Cardiac pacemaker. Wikipedia, CC BY-SA 3.0

14. ECG principle. Wikipedia, CC by 3.0

15. Sinus Rhythm. Wikipedia, Public domain

16. Sample EKG. Wikipedia, Public Domain

17. EKG leads. Wikipedia, Public Domain

18. Precordial leads. Wikipedia, Public Domain

19. Limb leads. Wikipedia, Public Domain

20. Limb leads. Wikipedia, Public Domain

21. Limb leads. Wikipedia, Public Domain

22. Sinus Rhythm. Wikipedia, Public domain

23. Sample EKG. Wikipedia, Public Domain

24. Vintage EKG machine. Wikipedia, Public Domain

25. Modern EKG machine. Wikipedia, CC by 3.0

26. What is a Holter? EKG + Time EKG Histogram

27. Holter. Wikipedia GNU Free Documentation License

28. Holter. Wikipedia GNU Free Documentation License

29. Holter. Wikipedia GNU Free Documentation License

30. Canine Holter. Wikipedia, Public Domain.

31. Holter. Wikipedia GNU Free Documentation License

32. Why I decided to do this?

33. Queue flashback!

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41. Problems • An EKG is just a snapshot of your

    heart at a specific moment. • A moment when you might not have symptoms. • Monitoring your heart requires a Holter. • You need an appointment and referral for a Holter study. • Holters fail. You have to start all over again. • Holters only work for 24 hours.

42. Realisation • An EKG is ADC sampling. • Holter is

    an EKG with storage and battery. Or a data logger. • I had all the knowledge to build an Arduino based data logger. • I could work on it 1 hour a day during my recovery.
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46. Challenges • Use off the shelves parts only. Orderwise known

    as “stuff-I-could-get-on-eBay” strategy. • Cheap. • Simple. • Use standard medical cables and electrodes. • Modular or breakout boards.

47. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management
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49. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

50. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

51. Bio Interface - Needs • No voltage but differential voltage

    reading • Signal amplification • Adaptive signal filtering • Analog to digital conversion

52. Bio Interface - Analog Devices AD8232 • $10-$20 USD •

    Built-in voltage comparators • Built-in amplifier • Built-in filtering • Power management • Cons: No ADC

53. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

54. Real Time Clock - Needs • Small • Battery or

    SuperCap backed up • Easy interface

55. Real Time Clock - Dallas DS3231 • $1 USD •

    I2C Interface • Unlike DS1302 and DS1307, has temperature compensated crystal and crystal oscillator • Has battery input and powerless timekeeping

56. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

57. Microcontroller unit - Needs • Low power • Analog to

    digital interface • Faster than bio interface sampling rate

58. Microcontroller unit - Arduino Nano • Clones at $4 USD

    • Atmel Atmega 328 at 16 MHz • Analog and digital pins • 32 KB Flash (minus 2KB bootloader) • I2C & SPI communications • UART TTL to USB

59. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

60. Power management - Needs • 5 volt output • High

    size and weight to power ratio • Low heat

61. Power management - Custom • GTL 18650 5300mAh Lithium Ion

    ($2 USD) • Lithium Ion charger module w/ output pins ($0.35 USD) • 3.7v to 5v voltage inverter ($0.50 USD)

62. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

63. Graphical User Interface - Needs • Small • Low power

    or low energy mode • Easy to interface

64. Graphical User Interface - Solomon Systech SD1306 • $5 USD

    • Multiple communication modes including I2C • OLED • Visibility • Pixel based • 2 x Push buttons

65. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

66. Storage - Needs • Fast • Detachable • Computer interface

    compatible

67. Storage - SDCard & module • $3 USD (card) +

    $1 USD (reader) • Cons: Fast modes need license. • SPI bus mode. This bus type supports only a 3.3-volt interface. This is the only bus type that does not require a host license. • 5V to 3V converter • 5V to 3V level converter

68. Communications SPI I2C or I2C

69. What is SPI The Serial Peripheral Interface bus (SPI) is

    a synchronous serial communication interface specification used for short distance communication, primarily in embedded systems. The interface was developed by Motorola in the late eighties and has become a de facto standard. Typical applications include Secure Digital cards and liquid crystal displays.

70. What is SPI SPI devices communicate in full duplex mode

    using a master-slave architecture with a single master.

71. What is I2C Short for Inter-IC, a type of bus

    designed by Philips Semiconductors in the early 1980s. Is used to connect integrated circuits (ICs).

72. What is I2C I2C is a multi-master bus, which means

    that multiple chips can be connected to the same bus and each one can act as a master by initiating a data transfer.

73. Block diagram MCU Bio Interface RTC Storage Graphical User Interface

    Power Management

74. Block diagram - Communications MCU Bio Interface RTC Storage Graphical

    User Interface Power Management Analog Digital I2C Digital I2C SPI

75. Organic interface - Connectors • Many types and subtypes ◦

    Snap ◦ Banana ◦ Suction ◦ Clip ◦ Limb clips ◦ Alligator • Easiest to work and with the most pros: Snap

76. Organic interface - Connectors

77. Organic interface - Leads • Build your own ◦ Source

    connectors ◦ Good wire gauge • Included leads ◦ Poor in all regards • Lead + electrode ◦ Not feasible

78. Organic interface - Leads • Professional ones ◦ Best connectors

    ◦ Best wire gauge ◦ Tangle resistant ◦ Labeled ◦ $20 USD ◦ Easy to interface

79. Organic interface - Electrodes • BIO Protech T815 ◦ Cloth

    ◦ Extended wear (day) ◦ Sweat resistant ◦ Cons: Painful to remove • BIO Protech T716 ◦ Foam ◦ Cons: Not water resistant • $20 USD for bag of 50

80. Organic interface - Electrodes • BIO Protech T815 ◦ Cloth

    ◦ Extended wear (day) ◦ Sweat resistant ◦ Cons: Painful to remove • BIO Protech T716 ◦ Foam ◦ Cons: Not water resistant

81. Firmware • Modular • Object oriented • 3 modes of

    operation: ◦ Realtime display ◦ Recording ◦ Serial port output

82. Libraries - Display: U8g2 • Large hardware support • Support

    fonts • Graphics drawing • Low memory display mode (tiled) • Custom icons • GUI widgets like menus and dialogs • Physical buttons interface and debouncing

83. Libraries - Storage: Bill Greiman’ SDfatlib • Non monolithic •

    Multiple classes: SdFat, SdBaseFile, SdFile, File, StdioStream, ifstream, ofstream • Mature • Fast • Economic memory usage

84. Libraries - RTC: Adafruit’s RTClib • Supports several Arduino MCUs

    • Provides access to the square wave pin • Cons: High memory consumption

85. Challenges and Tricks • Sampling rate reliability • Sample jitter

    • Fast OLED display updates • Heartbeat detection • BPM calculation • Interference filtering • Memory footprint reduction

86. Challenges and Tricks • Sampling rate reliability • Sample jitter

    • Fast OLED display updates • Heartbeat detection • BPM calculation • Interference filtering • Memory footprint reduction

87. Sampling rate reliability • Arduino’s crystal is subject to drift

    • Interrupt driven • Improve periodicity of readings • Increase sample rate

88. Sampling rate reliability - Solution Use the DS3231 square wave

    output pin to trigger Arduino’s hardware interrupt and do sampling in an ISR.

89. Sampling rate reliability - Solution The enable_interrupt function turns on

    the square wave pin and enables the Arduino hardware interrupt pin to call a callback function on the falling edge of the wave.

90. Sampling rate reliability - Solution By default, a 4 KHz

    square wave is used, triggering the ISR 4,000 times a second or once every 0.000244141 seconds. This, we’ll call RTC ticks.

91. Sampling rate reliability - Solution To get 100 samples a

    seconds, how many ticks between each? 1 / 100 / 0.000244141 = every 40.959937086 ticks

92. Sampling rate reliability - Solution

93. Sampling rate reliability - Solution

94. Sampling rate reliability - Solution

95. Sampling rate reliability - Solution MCU Main loop MCU RTC

    driven ISR ad8232 ad8232_buffer ad8232 interrupt_data_ready RTC

96. Sampling rate reliability - Solution Consumer Hardware timer Generator Buffer

    (FIFO Stack) Lock Realtime sampling and multithreading on the Arduino.

97. Recordings format

98. Recordings format FAT only allows 8.3 filenames.

99. Recordings format Unique non sequential filenames?

100. Recordings format Hexadecimal unixtime!

101. Recordings format

102. Recordings format Decimal to time_struct, to epoch, to datetime

103. Recordings format

104. Recordings format Unique up to a second of difference.

105. Heartbeat detection A heartbeat is not a spike but a

     wave

106. Heartbeat detection

107. Heartbeat detection

108. Heartbeat detection

109. Heartbeat detection We are interested in #2

110. Heartbeat detection

111. Heartbeat detection

112. Heartbeat detection

113. Heartbeat detection

114. Heartbeat detection

115. Heartbeat detection

116. Heartbeat detection

117. Heartbeat detection

118. Heartbeat detection

119. The build

120. First prototype

121. First prototype

122. First prototype

123. First prototype

124. First prototype

125. It’s ALIVE!

126. None

127. It’s ALIVE!

128. First prototype • 3 modes of operation • Pocket size

     • Total cost ~ $30 USD • 4 GB SD Card (vs. 128 MB commercial • 12 days battery life (vs. 1 day commercial) • Rechargeable via USB • Upgradeable via USB

129. First prototype • Total flash usage: 29KB • Total RAM

     usage: 500 bytes

130. The App

131. Creating an EKG journal A chart is good. A journal

     is better.

132. Creating an EKG journal Recording downloader Packaged program Historic recordings

     Metadata Graphical Tags Share
133. None

134. Not just a DMS, but also a platform

135. Features of interest Mayan Apps Generic templates Metadata Graphical previews

     Tags Email sharing Access Control

136. App - Requirements • Upload recordings • Preview/render recordings •

     Selection and trim • Conversion to archival version • Metadata, tagging, etc. • Search • Sharing

137. App

138. App - Registration

139. App - Registration

140. App - Registration

141. App - Models

142. App - Models

143. App - Models

144. App - Model views

145. App - Model views

146. App - Model views

147. App - Model views

148. App - Model views

149. App - Model views

150. App - Widget, dygraphs

151. App - Widget, dygraphs

152. App - API views

153. App - Capture form

154. App - Capture form

155. App - Capture form

156. App - Capture form

157. App - Capture form

158. App - Capture form

159. App - Capture form

160. App - Recording slices list

161. App - Recording slices previews

162. App - Recording slices comments

163. App - Recording slices categorization

164. App - Recording slices categorization

165. App - Recording slices categorization

166. App - Recording slices searching

167. App - Recording slices searching

168. App - Recording slices searching

169. Demo

170. What’s next? Future enhancements, ideas, wishes.

171. Improvements, wishlist • Smaller • Single board • More leads

     • Panic button • Remove RTC -> Interrupt • Wireless • Battery level & low battery indicator • Audible “beeps” • Power save mode, smart power on & off

172. Improvements, wishlist

173. Improvements, wishlist Mayan Box (Mayan on a battery powered, wireless,

     single board computer) + OpenHolter = ??

174. Improvements, wishlist Solar powered, last mile, electrophysiologist office.

175. Improvements, wishlist Solar powered, on-the-field, emergency electrophysiologist station.

176. Improvements, wishlist • Mayan Box combo • SBC and Mayan

     inside

177. Next prototype

178. Questions? Critiques Comments Suggestions

179. Thank you!

180. The OpenHolter Project: D.I.Y. Cardiometry with Arduino and Django. Roberto

     Rosario robertorosario.com