IO tools for biomedical images

A collection of tools for processing biological or medical images.

• 3D Segmentation Rendering
• Overlap heatmap color

3D Segmentation Render

This section includes steps with which we render the 3D segmentation results of [CShaper](https://www.nature.com/articles/s41467-020-19863-x). This is a customized framework to display our work but it maybe also valuable for showing other kinds of data.

Generally speaking, multiple softwares or applications are involved in rendering the result. The data flow follows *.nii.gz --> *.tif --> *.obi/*.mtl --> *.png, Specifically,

1. Save segmentation (here *.nii.gz) as indexed tiff image. (Code: save_indexed_tif)

2. Use Fiji plugin to extract 3D framework (*.obi) of the segmentation. If only one image needs to be be processed, the segmentation can be manually import and rendered with Plugins|Process|Show color surface; If a bunch of images are required, the Macros would be helpful. (Code: draw3DSnap.ijm)

3. The blender can import *.obj and even support user defined python script. Also, the python script can be used to process multiple images automatically. (Code: blender_script)

Example,

Overlay Heatmap

A transparent color map is overlaied on the raw image. For details, please refer to HeatMap. (Code: Heatmap.py)