setup_pl: User friendly way to setup whole brain pipeline analysis

In mjin1812/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Description

Asks user for setup information for wholebrain analysis. Generates a setup list of length 9 if the user is registering a partial brain or of length 18 if the user is mapping a whole brain. If a setup list already exists, calling this function will simply ask the user to verify setup info. Info can be changed if necessary. However, be conservative with changing setup parameters, especially if different users work on the same brain.

Usage

setup_pl(setup = NULL)

Arguments

setup

(optional) Allows the user to modify a setup list previously generated by this function.

Details

Descriptions of list elements for a partial brain.

1. Animal ID

2. User's Initials.

3. Registration channel image folder path (normally an autofluorescence channel)

4. Segmentation channel image folder path (can be different than the Registration channel)

5. Output folder to store data

6. All AP coordinates ranging from the first to last AP. User manually entered.

7. All z image numbers matching element 6. User manually entered.

8. Savepaths list containing paths to the data directories. Will be NULL until get_savepath() is run.

9. List of sorted image paths. Will be NULL until im_sort() is run.

Descriptions of list elements for a whole brain.

1. Animal ID

2. User's Initials

3. Registration channel image folder path (normally an autofluorescence channel)

4. Segmentation channel image folder path (can be the same as the Registration channel)

5. Output folder to store data

6. Spacing between adjacent z images (mm)

7. Spacing between registrations (mm). Default is 0.100, meaning registrations are performed every 100 um. Recommended input is are multiples of 0.100. Beware! Larger spacing between registrations means less manual work but less accurate mapping in the rostral caudal axis.

8. Integer step size between z-images used for segmentation. Default is 1 (1 skips no images, 2 skips every other, etc.).

9. First AP coordinate

10. First z image. Note: Keep all images of the stack together, even if the first usable image isn't 1.

11. Last AP coordinate

12. Last z image

13. AP coordinates of internal reference planes. Default coordinates are 1.91, 1.10, -.42, -0.93 , -1.94 , -2.95, -3.96. They correspond to PFC, NAc, antHyp, startHip, posHyp, VTA, PAG, respectively.

14. z image numbers matching AP coordinates (14). Will be NULL until choice() is run.

15. All AP coordinates ranging from the first to last AP. Will be NULL until interpolate() is run.

16. All z image numbers matching 16. Will be NULL until interpolate() is run.

17. Savepaths list containing paths to the data directories. Will be NULL until get_savepaths() is run.

18. List of sorted image paths. Will be NULL until im_sort() is run.

Value

setup is a list of length 7 or length 16 with parameters for the pipeline analysis.

mjin1812/SMART documentation built on Oct. 30, 2021, 7:25 p.m.