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Cortical Flatmap

This code here is designed to generate a flatmap visual representation with a image that is registered (transformed) to the Allen CCF.

How to use

Setting

input_immage

  • The image have to be registered to Allen CCF with upright coronal posterial to anterial both nii and tif are okay

output_folder

  • output location

output_name

  • name here is used as prefix for the final file name output will be nii

gaussian_preprocessing_pix

  • gaussian_preprocessing_pix = 0; no preprocessing
  • gaussian_preprocessing_pix = 4; 4 pixel blurring

projection_math

  • projection_math = 'maximum'; maximum
  • projection_math = 'average'; average

layer_specific

  • layer_specific = 0 meaning all layers together
  • layer_specific = 1 meaning you want to plot layer specific map

Layer_specific_list

  • Layer_specific_list = {["1" ], ["2", "3", "4" ], ["5" ], ["6" ]}; pick layers

Limitations

  • The brain need to oriented as x(image top to down) = D->V, y(image left to right) = L->R, z(image stack) = P->A.
  • The image need to be exact dimetion as the Allen CCF
  • The input image can be 10x10x10 um or 20x20x20 um

Environment

Matlab 2019a

Liscense

Free academic use.

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Yongsoo Kim lab

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