Python analysis pipeline for data measured with wire myograph 620M (Danish Myo Technology) exported from LabChart (AD Instruments). Calculates vascular contraction and relaxation responses from .txt files and produces summary figures and an Excel results table. Analysis condition: every event (reagent addition, rinse) has to be marked as a comment during recording in LabChart.

▶️ Run the analysis interactively in your browser (Google Colab — free, no installation):

Python and R scripts for local use are also available in this repository.

What it does

Parses time-series force recordings from 8-channel myograph experiments. Contraction and relaxation values are calculated from comment-anchored time windows:

• KCl 60 mM contraction — smooth muscle viability reference
• Phenylephrine (Phe) — α1-adrenergic contractility, either as a full cumulative dose-response curve (0.01–3 μM) or a single maximal dose (3 μM)
• Acetylcholine (ACh) — endothelium-dependent relaxation, expressed as % of submaximal Phe pre-contraction
• SNP — endothelium-independent relaxation (NO donor), expressed as % of second submaximal Phe pre-contraction

All results land in a single DataFrame (and one Excel sheet): absolute values in mN first, then all percentage values — so columns are easy to copy into GraphPad or R for statistics.

Files

myograph_colab.ipynb    — Google Colab notebook (upload/download via browser)
python/myograph.py      — standalone Python script (command line)
R/myograph.R            — R script (RStudio)
sample_data.txt    — sample LabChart export for testing

Usage

Colab Notebook

Click the link on the top of the page or import the notebook file in Google Colab via Github or file upload.

Python script (local)

pip install numpy pandas matplotlib openpyxl

Edit INPUT_FILE and OUTPUT_DIR at the top of python/myograph.py, then run:

python myograph.py

R script (RStudio)

install.packages(c("ggplot2", "writexl", "scales", "tidyr", "patchwork"))
source("R/myograph.R")

Edit INPUT_FILE and OUTPUT_DIR at the top of the script before running.

install.packages(c("ggplot2", "writexl", "scales", "tidyr", "patchwork"))
source("R/myograph.R")

Edit INPUT_FILE and OUTPUT_DIR at the top of the script before running. The plot opens in the RStudio Plots pane and is also saved as PNG.

Settings — the same across all three versions

The only section you need to edit is the settings block at the top, phenylephrine mode (dose-response or single-dose-induced maximal contraction) and comment labels. All three versions use the same parameters:

# Protocol mode
PHE_MODE = 'dose_response'   # or 'single_dose'

# Cumulative dose labels — match exactly what was typed in LabChart
PHE_LABELS = ['Phe0,01', 'Phe0,03', 'Phe0,1', 'Phe0,3', 'Phe1', 'Phe3'] #ignore if you use single_dose
ACH_LABELS = ['Ach0,001', 'Ach0,01', 'Ach0,1', 'Ach1', 'Ach10']
SNP_LABELS = ['SNP0,001', 'SNP0,01', 'SNP0,1', 'SNP1']

# Concentrations — must be in the same order as the labels above
PHE_CONC = [0.01, 0.03, 0.1, 0.3, 1.0, 3.0]   # uM
ACH_CONC = [0.001, 0.01, 0.1, 1.0, 10.0]        # uM
SNP_CONC = [0.001, 0.01, 0.1, 1.0]              # uM

# Fixed protocol markers — edit if your LabChart annotations differ
L_KCL60       = 'KCl60'    # KCl 60 mM addition
L_KCL60_END   = 'P2'       # rinse after KCl60
L_PHE_END     = 'PP'       # plateau marker after Phe (both modes)
L_PHE_SINGLE  = 'Phe3uM'  # single-dose Phe label (single_dose mode only)
L_SUBPHE      = 'subPhe'   # submaximal Phe before ACh
L_SUBPHE_END  = 'Ach0,001' # first ACh dose (= end of subPhe window)
L_SUBPHE2     = '2subPhe'  # submaximal Phe before SNP
L_SUBPHE2_END = 'SNP0,001' # first SNP dose (= end of 2subPhe window)
L_ACH_END     = 'P3'       # rinse after ACh
L_SNP_END     = 'K'        # end of recording

If a label doesn't match, the script raises an error listing all labels actually found in the file. In the Colab notebook, use Step 2 (comment preview) to check before running the analysis. In Python and R, the comment preview prints automatically at startup.

Output

• Excel — single sheet, metrics as rows (metric column), channels as columns (ch1–ch8). Absolute values (mN) first, percentage values below.
• PNG — 2×2 summary figure: Phe dose-response or bar chart, ACh relaxation (inverted Y), SNP relaxation (inverted Y), KCl viability barplot. Output filename matches the input .txt file.

Input file format

Standard LabChart tab-separated .txt export, decimal comma, 9 header lines. Each channel (1–8) is one aortic ring. Protocol events must be annotated with the #* prefix in LabChart (comment option) before export.