Combining membrane potential and calcium imaging in brain slices using the voltage sensitive dye ElectroFluor630 and the calcium indicator Calbryte520

README.md 2025-12-02 1 / 4 Calcium and Voltage Imaging Dataset This dataset contains multi-frame calcium imaging recordings acquired using four fluorescent calcium indicator dyes: Calbr, Cal520, Fluo4, and Fluo8. and one voltage sensetive dye called Ef630 Each file (.ome.tiff) represents a single recording consisting of 100 frames captured from a specific brain slice (hippocampus)and dye condition. Plus 2 other folder named nbqxap5 and ttx which are experimental conditions or pharmacological treatments applied during imaging. TTX: Tetrodotoxin – a sodium channel blocker, used to suppress action potentials. NBQX/AP5 (nbqxap5): Glutamate receptor antagonists – NBQX blocks AMPA receptors, AP5 blocks NMDA receptors. These files contain one .ome.tiff for calcium and voltage recording befor and after blockers(voltege is avrage of 7 recordings and calcium avrage of 2 recordings.) to monitor their effect on signal. Each recording tiff is 400 frames captured from an original 500 frames tiff file. Experimental Overview For each calcium dye: Three recordings plus one bleach recording were acquired then the sample was allowed to recover for 15 minutes and this protocol was repeated for: Calbr and Cal520 and ef630: 3 experimental cycles Fluo4 and Fluo8: 2 experimental cycles (these dyes fade away faster and signal degrade beyond 30 minutes) which mean for each slices of flou4,fluo8 we have 9 recordings and for calbr,cal520,ef630 12 recordings Ttx : 5slices and each slice has 4 recording Nbqxap5: 7 slice and 4 recording for each They were renamed for ease of processing as: S01 "calcium_before_ttx_": "r01", "voltage before_ttx": "r02", "calcium_after_ttx_": "r03", "voltage_after_ttx_": "r04", and same for nbqxap5. Experimental Metadata Field Description Institution / Lab [Laboratoire Interdisciplinaire de Physique(LIPhy), OPTIMA Research Group, 'Université Grenoble-Alpes et CNRS] Experiment Type Calcium imaging using fluorescent indicators and voltage sensetive dye ef630 Microscope [ Olympus XLPlan, 25x/1.05 W MP water immersion objective] Camera / Sensor [ KINETIX-M-C,TELEDYNE PHOTOMETRICS] README.md 2025-12-02 2 / 4 Field Description Acquisition Software [ Micro-Manager] Frame Rate [0.2 msecond per frame ,5 KHz] Exposure Time [0.2 ms] Resolution [ 512 × 512 pixels] Bit Depth [8-bit grayscale] File Format OME-TIFF (compatible with ImageJ/Fiji, Napari, Python) Date of Acquisition [ August–October 2025] 📁 Folder Structure As you download and unzip the folder: ├── calbr/ │ ├── calbr_s01_r01.ome.tiff │ ├── calbr_s01_r02.ome.tiff │ └── ... ├── cal520/ │ ├── cal520_s01_r01.ome.tiff │ └── ... ├── fluo4/ ├── fluo8/ ├── ef630/ ├── ttx/ ├── nbqxap5/ ├── loader.py ├── viwer.py └── README.md Data Organization Field Description Dye Fluorescent calcium indicator (calbr, cal520, fluo4, fluo8, ef630) and blocker(ttx ,nbqxap5) Slice (sXX) Tissue slice number (1–7) and 1-5 for ttx Recording (rXX) fluo4 and flou8 Recording index (1–9) calbr and cal520 and ef630 (1-12), ttx/nbqxap5 (1-4) Frames per file 100 (cropped 51–150) from 500 frames original and 400 for blockers Format OME-TIFF (.ome.tiff) Dimensions [frames, height, width] Naming convention: {dye/blocker}_s{slice:02d}_r{recording:02d}.ome.tiff Example: calbr_s01_r03.ome.tiff → CalbR dye, slice 1, recording 3. README.md 2025-12-02 3 / 4 How to View or Load the Data Each files contain tiff file hich can be load and viewed through ready to use software like ImageJ / FIJI however you can alos: 1. Viewing the Data (No Coding Required) Option A — Using the Viewer GUI (viewer.py) Download the full dataset folder and unzip it (e.g., C:\Dyes\calcium_dataset). Open the folder in File Explorer or double click on the viewer.py file or click right on it and choose Open in Terminal and just wait. A window will pops up that you can select the dye and slice and recording number and see the image. Use the frame slider below image to see each frames. Also You can open your cmd(command prompt) and type cd C:\Users\YourName\Desktop\project #your file directory (This opens Command Prompt inside the dataset folder.) Type: python viewer.py Wait a moment — the script will: Automatically install any missing libraries Open a window titled “Imaging Viewer” Inside the window: Choose your dye (Calbr, Cal520, Fluo4, Fluo8 or ef630) or blocker(ttx , nbqxap5) Select the slice and recording The image stack will load automatically Use the frame slider to browse through frames The stack shape (e.g., 100 × 512 × 512) is displayed at the bottom If Python is not installed in your system, you should first download it https://www.python.org/downloads/ you can check your system has installed python by simply type README.md 2025-12-02 4 / 4 python --version in your cmd. 2. Loading Data Programmatically (Researchers / Python Users) You can load recordings directly into Python or Jupyter notebooks or online on https://colab.research.google.com/using the loader.py module. then to monitor a specific dye, slice, and recording, simply copy and paste the code below. Example: from loader import load_recording base_path = r"C:/Dyes/calcium_dataset" #replace this part with your actual file path # select dye (Fluo4,Fluo8,Calbr,CAL520,ef630) or blocker, Slice number, Recording number stack = load_recording(base_path, "fluo4", 2, 5) print("Stack shape:", stack.shape) # (100, height, width) 3. MATLAB Users You can load .ome.tiff stacks directly in MATLAB using: stack = tiffreadVolume('calbr_s01_r01.ome.tiff'); imshow(stack(:,:,1), []);