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mask_generation.md

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  • On a machine with monitor, launch the maskingGUI. Run DATA_ROOTDIR=/home/yuncong/brainstem/home/yuncong/demo_data ROOT_DIR=/home/yuncong/brainstem/home/yuncong/demo_data THUMBNAIL_DATA_ROOTDIR=/home/yuncong/brainstem/home/yuncong/demo_data python src/gui/mask_editing_tool_v4.py DEMO998 NtbNormalized. Generate initial masks.
├── CSHL_data_processed
│   └── DEMO998
│       ├── DEMO998_prep1_thumbnail_anchorInitSnakeContours.pkl
│       ├── DEMO998_prep1_thumbnail_initSnakeContours.pkl
  • Modify input_spec.ini as (alignedPadded,NtbNormalized,thumbnail). python masking.py example_specs/DEMO998_input_spec.ini /home/yuncong/demo_data/CSHL_data_processed/DEMO998/DEMO998_prep1_thumbnail_initSnakeContours.pkl
├── CSHL_data_processed
│   └── DEMO998
│       ├── DEMO998_prep1_thumbnail_autoSubmasks
│       │   ├── MD662&661-F81-2017.06.06-12.44.40_MD661_2_0242
│       │   │   ├── MD662&661-F81-2017.06.06-12.44.40_MD661_2_0242_prep1_thumbnail_autoSubmask_0.png
│       │   │   └── MD662&661-F81-2017.06.06-12.44.40_MD661_2_0242_prep1_thumbnail_autoSubmaskDecisions.csv
│       │   ├── MD662&661-F84-2017.06.06-14.03.51_MD661_1_0250
│       │   │   ├── MD662&661-F84-2017.06.06-14.03.51_MD661_1_0250_prep1_thumbnail_autoSubmask_0.png
│       │   │   └── MD662&661-F84-2017.06.06-14.03.51_MD661_1_0250_prep1_thumbnail_autoSubmaskDecisions.csv
│       │   └── MD662&661-F86-2017.06.06-14.56.48_MD661_2_0257
│       │       ├── MD662&661-F86-2017.06.06-14.56.48_MD661_2_0257_prep1_thumbnail_autoSubmask_0.png
│       │       └── MD662&661-F86-2017.06.06-14.56.48_MD661_2_0257_prep1_thumbnail_autoSubmaskDecisions.csv
  • Re-launch masking GUI to inspect, correct the automatically generated masks, then export as PNGs.
├── CSHL_data_processed
│   └── DEMO998
│       ├── DEMO998_prep1_thumbnail_mask
│       │   ├── MD662&661-F81-2017.06.06-12.44.40_MD661_2_0242_prep1_thumbnail_mask.png
│       │   ├── MD662&661-F84-2017.06.06-14.03.51_MD661_1_0250_prep1_thumbnail_mask.png
│       │   └── MD662&661-F86-2017.06.06-14.56.48_MD661_2_0257_prep1_thumbnail_mask.png
  • Modify input_spec.ini as (None,NtbNormalized,thumbnail). Run python generate_original_image_crop_csv.py example_specs/DEMO998_input_spec.ini.
├── CSHL_data_processed
│   └── DEMO998
│       ├── DEMO998_original_image_crop.csv
  • Copy operation config template. cp $DATA_ROOTDIR/operation_configs/crop_orig_template.ini $DATA_ROOTDIR/CSHL_data_processed/DEMO998/DEMO998_operation_configs/crop_orig.ini. Modify crop_orig.ini.
  • Modify input_spec.ini as (alignedPadded,mask,thumbnail). Run python warp_crop.py --input_spec example_specs/DEMO998_input_spec.ini --op_id from_padded_to_none.
├── CSHL_data_processed
│   └── DEMO998
│       ├── DEMO998_thumbnail_mask
│       │   ├── MD662&661-F81-2017.06.06-12.44.40_MD661_2_0242_thumbnail_mask.png
│       │   ├── MD662&661-F84-2017.06.06-14.03.51_MD661_1_0250_thumbnail_mask.png
│       │   └── MD662&661-F86-2017.06.06-14.56.48_MD661_2_0257_thumbnail_mask.png