This guide will go through the steps to modify a texture used by Warframe via the OpenWF Bootstrapper.

Before we start: know what you're replacing. I am going to be using /Lotus/Interface/PolarityPoint.png as an example, which is the icon for the Vazarin polarity.
To explore textures, I can recommend using the GUI of Puxtril's Warframe Exporter.

1. Clone warframe-cache-tools.
2. Within your copy of warframe-cache-tools, you can now run pluto extract.pluto /Lotus/Interface/PolarityPoint.png to download & export the texture to the assets folder.
3. Head inside of the assets folder until you find PolarityPoint.png.dds.
4. Open the DDS file inside of a hex editor like HexEd.it or HxD and take note of the format, e.g. you will see the string DXT1 or DXT5 in the 6th row.
5. You are now free to modify the image however you want. Just take care that the file has the same name, dimensions/resolution, and format/encoding as seen before.
6. To build your assets, run pluto build.pluto within the warframe-cache-tools directory.
7. Finally, to get the assets into the game, you can copy the content (managed) folder from warframe-cache-tools into the OpenWF folder of your client. The Bootstrapper will automatically patch the game to use your modified content, and if you ever wanna stop using it, you can simply remove the client's content (managed) folder.