Requirements and Installation

Requirements & Installation

System Requirements

• Python ≥ 3.12 (3.14 recommended, official builds use 3.14)
• macOS, Linux, or Windows

Dependencies

Package	Purpose
numpy	Array computation
scipy	Optimisers (Levenberg-Marquardt, Differential Evolution), signal processing
matplotlib	Plotting (decay curves, lifetime maps, phasor plots)
xarray	Labelled N-D arrays for FLIM signals
phasorpy (0.10)	Phasor computation, calibration, cursor masking, spatial filtering, lifetime conversion
PyWavelets	Wavelet-based phasor denoising
inquirer	Interactive terminal prompts
ipywidgets + ipympl	Jupyter notebook interactive support
cellpose (≥ 3.0)	Deep-learning cell segmentation (Cellpose-SAM) for cell masking
opencv-python	Image I/O, resizing, and general image processing
openpyxl	Excel XLSX parsing for FLIM microscope software IRF extraction
pandas	Excel/XLSX IRF file parsing
tifffile	TIFF image I/O
tqdm	Progress bars

Installation

git clone https://github.com/alex1075/FLIMKit.git
cd FLIMKit
python install.py

install.py installs core requirements, then auto-detects and installs the right GPU backend (MLX on Apple Silicon, CUDA on NVIDIA, ROCm on AMD, CPU-only fallback). No flags needed for a standard install.

python install.py --dev      # also installs PyInstaller and test requirements
python install.py --dry-run  # preview commands without executing

Validate Installation

python validate_installation.py

Runs 10 checks: dependencies, module imports, XLIF parsing, stitching, fitting, phasor pipeline, per-tile fit pipeline, and GPU backend dispatch. All should pass.

Hardware Limits

python hardware_limits.py

Stress-tests the machine by ramping canvas sizes (64×64 → 4096×4096) and measuring fixed-tau GPU and free-tau CPU throughput. Reports peak pixels/second, RAM headroom, and estimated wall-clock times for common acquisition sizes. Useful for understanding what canvas sizes are feasible before starting a long batch run.