Workflows and Tools¶
These open-source repositories address specific microscopy analysis problems with FIJI/ImageJ macros, Python scripts, GPU-accelerated processing, and Imaris visualization resources. The descriptions below identify the data context, main workflow steps, software stack, and intended measurement value.
Large-Volume Processing and Quantification¶
LLSM Batch Preprocessing
Data
Large-volume light-sheet microscopy raw image data.
Workflow
Suppress background noise, enhance nuclei signal, and smooth structural boundaries before spot detection or anatomical segmentation.
Stack
FIJI/ImageJ macros | GPU-accelerated processing | Imaris
Value
Prepares large datasets for more reliable downstream detection, segmentation, visualization, and quantification.
Yeast Nuclear Puncta Cell Counter
Data
Yeast fluorescence microscopy images containing nuclear puncta.
Workflow
Automate puncta detection and quantitative counting in microscopy images.
Stack
Open image analysis pipeline
Value
Supports repeatable measurement of nuclear puncta across image datasets.
Dynamics and Colocalization¶
TF Nuclear Translocation Analysis
Data
Time-lapse microscopy data with segmented and tracked single cells.
Workflow
Refine cell trajectories and quantify stress-induced Dot6-GFP nuclear translocation.
Stack
Python | FIJI/ImageJ | TrackMate-Cellpose
Value
Connects single-cell motion histories with quantitative transcription factor localization measurements.
TIRF Vesicle Colocalization Analysis
Data
Time-series TIRF microscopy images of Glut10 and Rab5 vesicles.
Workflow
Detect, identify, and track colocalized vesicles across time.
Stack
Python
Value
Supports quantitative analysis of vesicle colocalization and dynamics near the cell membrane.
Morphology and Visualization¶
Cell Distance Mesh Generator
Data
Microscopy-derived cell positions or regions.
Workflow
Generate distance meshes between cells for spatial analysis and visualization.
Stack
FIJI/ImageJ macro
Value
Makes relative cell spacing available for quantitative visual interpretation.
Central Nuclei Muscle Analyzer
Data
Muscle cross-sectional microscopy images.
Workflow
Analyze nuclear localization and quantify centrally located nuclei in muscle fibers.
Stack
FIJI/ImageJ macro
Value
Automates a repeated morphology measurement used in muscle image analysis.
ImageJ Hot LUT Palettes
Data
Quantitative microscopy images visualized in Imaris.
Workflow
Apply Imaris palette files based on familiar FIJI/ImageJ hot lookup tables.
Stack
Imaris palettes
Value
Provides reusable, consistent color mapping for microscopy visualization.