Update Log

• 2024-04-15: version 1.0.0, first release.
• 2024-04-16: version 1.1.0, add demos.

Demo

The following videos are the results from a single experiment. (P.S.: w3_ND16_2024-04-10_23-28-30 in our server).

Check full videos of this experiment on YouTube.

• Original
• Soma + Axon + Dendrite
• Soma
• Axon + Dendrite

User Guide

Workflow

up-stream.m

• .tif -> is_outlier.mat, .mp4, intensity.mat

down-stream.m

• 2 is_outlier.mat -> is_outlier_union.mat

• intensity.mat, is_outlier_union.mat ->intensity.mat, intensity_volume.mat

• 2 intensity_volume.mat -> figures of red and green channel

The Structure of the Data Folder

Data
│
├── w1
│   ├── 0_Camera-Red_VSC-10629
│   │   └── *.tif
│   └── 1_Camera-Green_VSC-09321
│       └── *.tif
│
├── w2
│   ├── 0_Camera-Red_VSC-10629
│   │   └── *.tif
│   └── 1_Camera-Green_VSC-09321
│       └── *.tif
│
├── w3
│   ├── 0_Camera-Red_VSC-10629
│   │   └── *.tif
│   └── 1_Camera-Green_VSC-09321
│       └── *.tif
...

The Selection

When using up-stream.m, select a folder of the w1 level.

When using down-stream.m, select a folder of the Data level.

Principle

How to Get the Intensity?

Answer: Use binarization.

note:

• How to detect outliers? (Don't need fine-tune)

  • Tukey test of the number of bright pixels of certain binary frame. IQR_index = 1.5
  • Tukey test of the intensity of bright pixels of certain binary frame. IQR_index = 1.5
  • Tukey test of the intensity_volume of certain volume. IQR_index = 3
  • Tukey test of the diff or ratio. IQR_index = 3

• How to deal with outliers?

  • make them to be nan.

How to Split the Soma and the Neurite (Axon + Dendrite)?

Answer: Use opening.

tune

super-parameter

• sense
• disk_r

note:

• Usually, $sense = 0.2$ is OK. In other words, you don't need to fine tune this super-parameter.
• $disk_r$ is needed to changed. You must tune it to split the soma and the neurite of the template channel. $disk_r \in {3,4,5,6,7,8}$

template

Requirements

• for the soma template: the soma and the neurite are easy enough to be split.
• for the neurite template: the neurite is brighter than the other channel.
• for the all template: the soma and the neurite are brighter than the other channel.

For example, in our taxis project in 2023/11, the green channel is brighter than the red channel, so

• the red channel is used as the soma template.
• the green channel is used as the neurite template.
• the green channel is used as the all template.

halo

Use opening to remove the halo of the soma after digging out it from the original BW.

How to Split Worms When Having Multiple Animals?

First, we must have a template for the whole neuron, otherwise, the affect of noise will be much more severe.

I use this criteria: in certain frame, for certain worm, choose the channel which has more bright pixels!