First you need to setup the Cartridge Reader Shield's config switches like so.
Then insert the MX29F1610 flashrom into the SOP44 ZIF socket, plug the ZIF socket into leftmost position of the 8bit flashrom adapter and finally plug the flashrom adapter into the cart reader.
You also have to adjust the two SMD switches both to the top position.
In the main menu first select "Flashrom Programmer" and then choose "8bit adapter".
To program the flashrom you need to erase it, then do the blankcheck and finally select write to flash it with your rom.
While writing a rom to the flashrom the led should blink constantly until the flashing process is completed.
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Cart Reader V5
Overview
Supported Systems
List of user-created Adapters
Community Discord Server
Build Guide
Recommended Tools
What to order
How to build
More Information
How to order a PCB
How to flash the Arduino
Flashing the snesCIC
Preparing the SD Card
Automatic Voltage Selection
Real‐Time Clock
Advanced
Troubleshooting
Calibrating the ClockGen
Designing your own Adapters
Serial Monitor
Savegame Conversion
Older Revisions
About
Cart Reader V4
Cart Reader V3
Cart Reader V2
Cart Reader V1
Firmware Archive
Nintendo 64
Read N64 cartridge
Reading a Controller Pak
Reflashing N64 Repros
Reflashing a Gameshark
Super Nintendo
Reading SNES/SFC carts
Reflashing NP carts
Reflashing SNES/SFC Repros
Reflashing BSX 8M carts
NES and Famicom
Dumping NES Games
Adding auto mapper to a game
Game Boy
Reading a Game Boy rom
Reflashing NP GB Memory carts
Writing custom flashcarts
Game Boy Advance
Reading a GBA save game
Reflashing GBA repros
SEGA
Reading Mega Drive Genesis games
Reading Master System games
Other
Flashrom Programmer
Flash-Adapter
AM29F016-AM29F032
MX29F1610
MX29L3211
MX29LV160
MX29LV320
S29GL032
39F040 PLCC32