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@@ -1,26 +1,32 @@
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[Normal](#normal)
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[1 Image patch extract](#1-image-patch-extract)
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+[2 Prediction](#2-prediction)
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+[3 Heatmap stitching](3-heatmap-stitching)
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-2. prediction
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-3. heatmap stitching
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-
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-[tasks](#tasks)
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-
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-My Hello, this is some text to fill in this, [here](#place-3), is a link to the second place.
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-My Hello, this is some text to fill in this, [here](#place-2), is a link to the second place.
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-
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-## Title
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+# 1 Image patch extract
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+The following commands launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup tables for every HDF5 file.
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+## Without color normalization
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+qsub split_main.sh ./config_testing.txt
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+qsub split_main.sh ./config_normal.txt
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+qsub split_main.sh ./config_tumor.txt
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-### Place 1
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+## With color normalization
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+qsub split_main.sh ./config_testing_cn_true.txt
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+qsub split_main.sh ./config_normal.txt
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+qsub split_main.sh ./config_tumor.txt
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-Hello, this is some text to fill in this, [here](#place-2), is a link to the second place.
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+## Creating lookup tables
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+bash create_lookup_grp.sh ./config_testing.txt
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+bash create_lookup_grp.sh ./config_normal.txt
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+bash create_lookup_grp.sh ./config_tumor.txt
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-### Place 2
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+The lookup tables are created only once.
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-Place one has the fun times of linking here, but I can also link back [here](#place-1).
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+# 2 Prediction
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-# Place 3
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+# 3 Heatmap stitching
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+
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qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
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@@ -70,11 +76,6 @@ total 278G
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[mikem@betsy02 split_wsi]$ ls -1 /scratch/wxc4/CAMELYON16-training/normal | wc -l
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159
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-<a name="tasks">
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- my tasks
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-</a>
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-
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-# 1 Image patch extract
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location of the bouding box
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