Hello, I am currently working on a neuron mRNA quantification project. In the big picture, I want to extract information from single molecule fluorescence microscopy images of neurons. The image above is an example. I would really want to perform my entire project in Napari and Python.
The information I need include the distribution (distance from nucleus) of mRNA, intensity of mRNA, etc. As a result, I would like to achieve the functions listed below:
- Stretch/straighten the dendrite so I can later calculate its distance from nucleus simply using the two coordinates. (Otherwise, it’s hard to find distance as the dendrites are curved paths.)
- Create outlines of all the dendrites for each neuron.
- Identify and Count mRNAs using image analysis. (Perhaps by setting a threshold.)
- Record the coordinates of each mRNA (white dots in the image).
Pipeline B (Thank you for suggesting this @jni ):
- Create outlines of dendrite.
- Segment and skeletonize the dendrites.
- Identify mRNAs and count along the skeleton (the segment that each mRNA belongs to will indicate its distance from nucleus).
For pipeline A, I wonder if Napari can achieve step 1 - straighten the dendrite. I am currently relying on ImageJ for that task and my programming skills do not allow me to create program that would automatically transform image to straighten it.
Another great challenge for me is how to identify mRNAs using Napari and Python. The only way I could think of is by setting min and max threshold and size limit for the program to determine whether a signal is mRNA. However, this is probably inaccurate, as signals of mRNA need to be fit on Gaussian Curves instead of simply setting threshold. Does anyone know any existing plugin or library in Napari or Python that can achieve that (similar to FishQuant in MatLab)?
Any help or insights will be greatly appreciated. Thanks