Exporting from UCSF Chimera

1. You need to use original chimera because it saves nested obj files. UCSF Chimera
2. Your script should

• open all the files,
• set voxelSize (if needs to be adjusted) volume # voxelSize 0.065,0.065,0.29;
• set the step volume # step 1;
• set the level, volume #0 level 0.0562;
• and then save it as an .obj: export ${exportPath}/mitochondria-M1.obj;

3. Example template:

const exportPath = '/Users/meganr/Dropbox/visual_cell_maker_files/objs-to-process'
module.exports = (mitosis, structure, voxelSize, memLevel, dnaLevel, structureLevel) =>
  `open /Users/meganr/Dropbox/visual_cell_maker_files/${structure}/${mitosis}/*.tiff;

volume # voxelSize ${voxelSize};

volume # step 1;
volume #0 level ${memLevel};
volume #1 level ${dnaLevel};
volume #2 level ${structureLevel};

export ${exportPath}/${structure}-${mitosis}.obj;

close all;

ao-baking

1. Open C4D
2. In UV-editing mode select 'UV Mesh' and then 'Show UV Mesh' (we tried to script this, but it doesnt seem to work)
3. Go back to standard/startup view if you want to watch the console.
4. Run script 'visual-cell.py'

Editing the script

Things you'll need to change:

• Input path (where the Objs are located, you can use the dropbox folder if you have that locally)
• Output path (where you are going to save these, it needs the actual file structure to exist, so you can copy my dropbox folder. It will overwrite exisiting images.
• fileNames (the structures + mitotic stages you want to process)