We use a 3rd-party tool which generates STL files with a specific medical coordinate system (either RAS/LPS for those interested).

Our software can only load the 3D meshes in OBJ format but whenever we load an STL into Blender and export as OBJ, it appears upside down and back to front. Worse, our other software emits metadata for annotations in the same coordinate system (as JSON/XML), and these are now garbage as they're not in the same coordinate system as the resultant OBJ.

Given we have explicitly defined coordinate systems we need to use, how can we get Blender to play nice? I have done a little googling and it seems Blender enforces its own axes which cannot be reconfigured but why does this mean it changes our X->Y, or whatever is happening?

Perhaps we can find a standard transform to apply to every model to counteract this but we would want that baked into the vertex positions not stored as a transform in the OBJ file (if OBJ even supports that?)

Thanks for any help.


2 Answers 2


In the obj exporter in blender 2.76 I have axis settings like that:


If you want to export your object with an origin other than (0,0,0), you can move the object so that origin will in the desired location before exporting.

Here's how to do it:

  1. Select the object you want to export in the 3D view.
  2. In the 3D View header, select "Object" > "Set Origin" > "Geometry to Origin" from the menu.
  3. This will move the object's origin to the center of its geometry. You can now move the object to the desired location by translating it in the 3D view using the move tool (shortcut G).
  4. Once the object is in the desired location, go to File > Export > Wavefront (.obj) to export your object as an OBJ file.
  5. In the export options, make sure the "Selection Only" box is checked so that only the selected object will be exported.
  6. In the "Objects as OBJ Objects" section, make sure the "Objects Origin" option is selected.
  7. Set the desired export location and filename for your OBJ file, and click "Export OBJ".

This should export your selected object as an OBJ file with its origin at the location you moved it to in step 3.


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