Merge pull request #2 from aaronbwong/master

Master
aaronbwong · Oct 7, 2024 · 5b3b24e · 5b3b24e
2 parents 5d241d0 + 665de93
commit 5b3b24e
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Showing 7 changed files with 78 additions and 286 deletions.
diff --git a/readme.md b/readme.md
@@ -9,4 +9,11 @@ This is the readme file accompanying the analysis pipeline for a anatomical trac
 
 ## Dependency
 - AP_histology requires "Curve Fitting Toolbox"
-- AP_histology requires [ColorBrewer/BrewerMap](https://github.com/DrosteEffect/BrewerMap) by DrosteEffect
+- AP_histology requires [ColorBrewer/BrewerMap](https://github.com/DrosteEffect/BrewerMap) by DrosteEffect
+- DeepSlice
+
+
+## Installation of DeepSlice
+- Python 3.7 is needed (not later, e.g. 3.11 as of Nov 2023) 
+- This can be done by installing miniconda or anaconda (search for installation file from archive)
+- Then `pip install DeepSlice` should work.
diff --git a/src/alignment/test_histology_pipeline.m → src/_general/test_histology_pipeline.m b/src/alignment/test_histology_pipeline.m → src/_general/test_histology_pipeline.m
@@ -11,8 +11,11 @@
 
 % -- Data specific ---
 im_path = 'W:\AnalyzedData\Histology\2023-141-09279\FullSize8bitTIFFs\j3';
-slice_path = 'W:\AnalyzedData\Histology\2023-141-09279\downsampledImages\j3';
+im_path = '\\borstlab-nas1\Aaron\EpiFluoData\2021_EpiFluoData\2017-628_AAVRetroICInj\2017-628';
+slice_path = 'W:\AnalyzedData\Histology\2023-141-09279\downsampledImages\j3_old';
+slice_path = 'W:\AnalyzedData\Histology\2017-628_test';
 prefix = '2023-141-09279-j3';
+prefix = '2017-628_test';
 % --------------------
 
 %%
@@ -65,7 +68,7 @@
 %% 3) Align CCF to slices
 
 % Find CCF slices corresponding to each histology slice
-% AP_grab_histology_ccf(tv,av,st,slice_path);
+AP_grab_histology_ccf(tv,av,st,slice_path);
 slice_plane_fn = [slice_path,filesep,'DeepSliceResults_normAngle_ordered_spacing_extrapolated.xml'];
 AP_grab_histology_ccf(tv,av,st,slice_path,slice_plane_fn)
 

diff --git a/src/image-preparation/AW_process_histology.m b/src/image-preparation/AW_process_histology.m
@@ -194,7 +194,9 @@ function AW_process_histology(im_path,resize_factor,slice_images,save_dir,prefix
 
     % Write all slice images to separate files
     disp('Saving slice images...');
-    save_slice_images(im_fn, resize_factor, im_rgb, save_dir,prefix);
+    flipHori = zeros(n_im,1);
+    rotate90CW = zeros(n_im,1);
+    save_slice_images(im_fn, resize_factor, im_rgb, save_dir,prefix,rotate90CW,flipHori);
     disp('Done.');
 
 

diff --git a/src/image-preparation/AW_reorderHistology.asv b/src/image-preparation/AW_reorderHistology.asv