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histology_to_ara's Introduction

Histology_to_ARA

Registration of a brain slice to the Allen Reference Atlas

Dependencies

Steps

1. In MoBIE, load the ARA (Use Mobie (see above) in expert mode)

1.1. Select plane corresponding to histology

1.2. Log transformation and copy to .txt file

1.3. Create screenshot WITH DEFAULT PARAMETERS. For 25um/pixel atlas this is 22.619um/px

1.4. Save text file and screenshot with the same names (ending in '.txt' and '_ARA.tif' as the histology in the same folder)

2. Register the histology to screenshot (e.g. python folder_register_ARA_to_histology.py 'path_to_000_Slices_for_ARA_registration')

3. Transform (2D to 3D) points to ARA (e.g. python points_transformation.py 'path_to_dataframe')

This dataframe is generated with Inmuno_4channels_analysis.ipynb in CellProfiler_AnalysisPipelines - https://github.com/HernandoMV/CellProfiler_AnalysisPipelines

4. Display points in ARA. use .ijm script in FijiCustom repo.

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