Segmentation and Reference Point Detection for Laser Capture Microdissection (LMD)
Project Summary
This repository contains the code for a Cellpose-SAM & pyLMD project dedicated to automating cell boundary and reference point detection in microscopic images used for Laser Capture Microdissection (LMD).
The primary function of this repository is to identify the boundaries of target cells and detect ...
Modified workflow to perform Voronoi segmentation, based on https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2.
Input requirements:
- RA: -- right ascension in degrees as a float number.
- Dec: -- Declination in degrees as a float number
- Radius: -- the radius of the cone to be queried in arcminutes as a float number
- Pixel size: -- the size of the pixel in arcseconds
- Band: -- the band (channel) of the image: g, r, z, i
The present workflow allows to perform 2D spots/blobs detection on specific channel and stack of an image. Images will be directly fetched from IDR by including the IDs. A pre-processing steps with histogram normalization is performed before the blobs detection.
Associated Tutorial
This workflows is part of the tutorial Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines, ...
Generic workflow to perform Voronoi segmentation. Input requirements:
- Image: -- Preferably lighter objects on a darker background for the mask to work well. -- Format: .tiff, stored in planar RGB format, not interleaved (http://avitevet.com/uncategorized/when-to-use-it-interleaved-vs-planar-image-data-storage/).
- Seeds: -- White seeds on a black background -- Format: .tiff
Associated Tutorial
This workflows is part of the tutorial [Voronoi ...
Tests 
Download