Unable to track probes without fixed lengths

[skrigel]

Hi,

Thank you for all of your help from my last discussion and the great work you’ve been doing. We’ve made some good progress in visualizing all of the scenes for a subject against the atlas, but it seems we’ve been slightly misusing the probe interface. Our intention is to match a section of a probe to one atlas slice, so we want to track probes with no fixed length. Because real brain tissue cuts are angled, portions of each probe might be located in a different atlas section. Being able to track a probe with no fixed length would allow us to identify the true start and end of the probe.

Might it be possible for you to incorporate a drawing tool that doesn’t have a fixed length so that we can manually track the probe in between scenes? We would be happy to contribute our efforts to the package if it would be helpful.

We have written and attached some code to visualize the position of a probe against the atlas using the current iteration of HERBS, and I have also included the sort of visualization we intend to use it for. Ideally, we would be tracking pieces of a probe rather than one probe per scene.

Thank you!

This is an example of one subject with four scenes, but we could amend our interface to be able to plot multiple animals at once:

What we are trying to do with HERBS would allow us to produce a plot with pieces of probes, as demonstrated by the blue lines in this image:

Code used to generate the plot:
visualize_probe_scenes.txt

[JingyiGF]

Hi, there is a drawing functionality in HERBS although I am not sure if that is what you want. You can subtract the start and end point from the saved drawing object to make it as parts of a probe. And I am sure you know how to get the brain region if you want. Have you tried? Since you are expert in Python, you are very welcome to submit a pull request if you would like to contribute to HERBS.