List of fixes for brains in the pipeline process

DK61

1. 226 needs fixing. Do this:
   1. make a backup of CH1/full/226.tif
   2. get size of preceding image with: identify 225.tif
   3. push tissue down the image with: convert 226.tif -background black -gravity South -extent 33456x70403 tiff64:226.out.tif
   4. delete existing 226.tif in CH1/thumbnail/ and CH1/normalized and CH1/thumnail_cleaned and CH1/thumbnail_aligned
   5. create new thumbnail with convert 226.out.tif -resize 3.125% -compress lzw ../thumbnail/226.tif
   6. rm CH1/full/226.out.tif
   7. recreated the normalized and masks and cleaned files.
   8. rm the 2 elastix directories 227_to_226 and 226_to_225
   9. rerun create_elastix and create_alignment. The results should be good. Once they are good, repeat the above process with CH2 and CH3

DK63

deletion and padding - done on CH1,2

1. Copy 012.tif (DK63_slide008_2021_07_06_11465_S1_C1.tif) to 011.tif (DK63_slide007_2021_07_05_11448_S4_C1.tif)
2. copy 225.tif (DK63_slide066_2021_07_03_11384_S2_C1.tif) to 224.tif (DK63_slide066_2021_07_03_11384_S1_C1.tif)
3. copy 235.tif (DK63_slide068_2021_07_03_11382_S4_C1.tif) to 236.tif (DK63_slide069_2021_07_04_11387_S1_C1.tif)
4. copy 238.tif (DK63_slide069_2021_07_04_11387_S3_C1.tif) to 239.tif (DK63_slide069_2021_07_04_11387_S4_C1.tif)
5. Copy 442.tif (DK63_slide118_2021_07_06_11482_S3_C1.tif) to 443.tif (DK63_slide118_2021_07_06_11482_S4_C1.tif)
6. copy 445.tif (DK63_slide119_2021_07_06_11483_S1_C1.tif) to 444.tif (DK63_slide118_2021_07_06_11482_S5_C1.tif).

mask cleaning

1. Alignment problem between 223 and 224, 223 is pretty awful,
2. Alignment problem between 35 and 36
3. Clean dot on 103 upper left - done
4. Clean dot on 223 lower left - done
5. Clean dot on 357 top right - can't get to it.
6. Clean dot on 360 lower right - done
7. Clean white arc on 438 upper right - done