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README.md
base-visual-cell-maker-file.c4d
chimera-script.md
visualcell.py

README.md

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 ${exportPath}/mitochondria-M1.obj;
  1. Example template:
const exportPath = '/Users/meganr/Dropbox/visual_cell_maker_files/objs-to-process'
module.exports = (mitosis, structure, voxelSize, memLevel, dnaLevel, structureLevel) =>
  `open /Users/meganr/Dropbox/visual_cell_maker_files/${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)