Icon

cell-segmentation-worker

Cell Segmentation (Worker)

The workflow aims to segment cell nuclei from cytoplasm. As a first step the images need to be preprocessed by splitting the channels into separate columns, nuclei and cytoplasm. To correct for background staining and reduce noise, we are performing a background subtraction of the nuclei channel and also apply Gaussian smoothing.

For segmentation, we first use the Otsu threshold method to distinguish between foreground and background. Afterwards we identify and label connected components (=nuclei) using the Connected Component Analysis node. Subsequently, we remove cell clumps and too small nuclei. As a last step, we perform a Voronoi based segmentation that identifies and labels the corresponding cytoplasm to the already labeled nuclei.

This workflow performs a cell segmentation routine on images as follows- Receives a list of image files as a KNIME Table and chunk information which determines the location of the results- Perform cell segmentation routine on those images - Writes the results to a KNIME Table under a result directory created next to the first image file. (The result KNIME Table file is named according to the chunk information received from the caller workflow)- Returns a path to the written KNIME Table containing the results list of fileschunk info Image Reader(Table) Segmentation Preprocessing WorkflowService Output Write Results WorkflowService Input WorkflowService Input Prep This workflow performs a cell segmentation routine on images as follows- Receives a list of image files as a KNIME Table and chunk information which determines the location of the results- Perform cell segmentation routine on those images - Writes the results to a KNIME Table under a result directory created next to the first image file. (The result KNIME Table file is named according to the chunk information received from the caller workflow)- Returns a path to the written KNIME Table containing the results list of fileschunk info Image Reader(Table) Segmentation Preprocessing WorkflowService Output Write Results WorkflowService Input WorkflowService Input Prep

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
On NodePit since: 2022-04-26
Last update: 2024-04-24
Created with KNIME version: v4.5.2
Tags: cell segmentationimage processingmicroscopy

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!