ColonyQuant/run_colonyquant_pipeline.sh at main · KidderLab/ColonyQuant · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
#!/usr/bin/env bash
set -euo pipefail

# ================================
# ColonyQuant full analysis pipeline
# ================================

# Input and output paths
AP_DIR="examples/images"
OUT_DIR="examples/output"

V4_DIR="${OUT_DIR}/v4_figs"
V11_DIR="${OUT_DIR}/v11_figs"
FD_DIR="${OUT_DIR}/feature_distributions"
CA_DIR="${OUT_DIR}/comprehensive_analysis"

# Create output directories
mkdir -p "${OUT_DIR}" \
         "${V4_DIR}" \
         "${V11_DIR}" \
         "${FD_DIR}" \
         "${CA_DIR}"

echo "[1/6] Quantitating AP-stained colonies"
colonyquant quantitate \
  --ap-dir "${AP_DIR}" \
  --block-size 51 \
  --offset 5 \
  --min-area 300 \
  --output "${OUT_DIR}"

echo "[2/6] Computing morphometric features"
colonyquant morphometrics \
  --ap-dir "${AP_DIR}" \
  --output-dir "${OUT_DIR}"

echo "[3/6] Running v4 visualization"
colonyquant visualize-v4 \
  --data-dir "${OUT_DIR}" \
  --out-dir "${V4_DIR}" \
  --features3 Log2Area "Mean Intensity" Circularity \
  --features2 Log2Area "Mean Intensity" \
  --grid_size 300 \
  --shapes

echo "[4/6] Running v11 visualization"
colonyquant visualize-v11 \
  --data-dir "${OUT_DIR}" \
  --out-dir "${V11_DIR}" \
  --features3 Log2Area "Mean Intensity" Circularity \
  --features2 Log2Area "Mean Intensity" \
  --grid_size 100 \
  --contours \
  --mosaic \
  --heatmosaic \
  --heatmap_size 200 \
  --global_clusters 100 \
  --cluster_analysis

echo "[5/6] Generating feature distribution plots"
colonyquant feature-distributions \
  --data-dir "${OUT_DIR}" \
  --out-dir "${FD_DIR}"

echo "[6/6] Running comprehensive analysis"
colonyquant comprehensive-analysis \
  --data-dir "${OUT_DIR}" \
  --out-dir "${CA_DIR}"

echo "✔ ColonyQuant pipeline completed successfully"