Flash Android Factoryimage without loss of Data ....

... with fastboot (works fine with eg. Android 6.0.0)

Make sure your computer recognizes your device by typing: fastboot devices

If not, then try this:

# reboot into fastboot mode
adb reboot bootloader

# grab you fastboot/bootloader device ids
lsusb
> Bus 001 Device 035: ID **18d1:d00d** Google Inc.

# install the ids into /etc/udev/rules.d/99-android.rules
SUBSYSTEM=="usb", ATTR{idVendor}=="18d1", ATTR{idProduct}=="d00d", MODE="0666", OWNER="username"

# restart udev
/etc/init.d/udev restart

# try fastboot (only on bootloader mode)
fastboot devices

Unlock your bootloader (if you have not already done so): fastboot oem unlock
You will see a prompt on your device. This will wipe your entire device (including the /sdcard folder). Accept. Note: you use the volume keys to change the option and the power button to accept. You cannot use the touch screen.
#Reboot by typing: 
fastboot reboot-bootloader
#Flash the bootloader: 
fastboot flash bootloader bootloader-mako-makoz10o.img (or whatever the name of the bootloader image is).
#Reboot: 
fastboot reboot-bootloader
#Flash the radio:  (if available)
fastboot flash radio radio-mako-m9615a-cefwmazm-2.0.1700.48.img (or whatever the name of the radio image is).
#Reboot: 
fastboot reboot-bootloader
#Flash the system partition: 
fastboot flash system system.img
Optional, but read note. Flash the data partition: 
fastboot flash userdata userdata.img Note: this command will wipe your device (including /sdcard), EVEN if your bootloader is already unlocked.
#Flash the kernel/ramdisk: 
fastboot flash boot boot.img
#Flash the recovery partition: 
fastboot flash recovery recovery.img (don't flash if you have a custom recovery rom)
#Flash the vendor: (if available)
fastboot flash vendor vendor.img
#Erase the cache partition: 
fastboot format cache
#Reboot: 
fastboot reboot
Done! The first boot will likely take quite a bit longer than you are used to, as Android builds the Dalvik cache. 

#Reboot:
adb reboot bootloader
#Flash the recovery partition: 
fastboot flash recovery twrp-2.8.7.0-mako.img (or whatever the name of the recovery image is).
#Reboot: 
fastboot reboot-bootloader
#Optional flash SuperSu with your favorite RecoveryROM to have rootaccess

#Reboot to Recovery from fastboot (eg. if the Volumebuttons are defect)
fastboot boot recovery.img (or whatever the name of the recovery image is).