Bright field microscopy


CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

has function

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

The recent version requires images of a lateral position. It is important that the position is precise since deviation may confound with feature annotations. Images from any source can be used. However, depending on the image properties parameters may have to be adjusted. Furthermore, images obtained with normal microscope and not using an automated position system with embryos in glass capillaries require conversion using a KNIME workflow (the workflow is available as well). As a result of the analysis the software provides JSON files that contain the coordinates of the features. Coordinates are provided for eye, fish contour, notochord , otoliths, yolk sac, pericard and swimbladder. Furthermore, pigment cells in the notochord area are detected. Additional features can be manually annotated. It is the aim of the software to provide the coordinates, which may then be analysed subsequently to identify and quantify changes in the morphology of zebrafish embryos.

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HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.


automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

maars workflow from publication



Spot detector detects and counts spots, based on wavelet transform.

- Detects spots in noisy images 2D/3D.
- Depending on objective, spots can be nuclei, nucleus or cell
- Versatile input: sequence or batch of file.
- Detects spot in specific band/channel.
- Multi band labeling: automaticaly creates ROIs from one band and count in the same or an other band.
- Filters detection by size.
- Sort detection by ROIs
- Output data in XLS Excel files: number of detection by ROIs, and each detection location and size.
- Outputs withness image with ROIs and detection painted on it.
- Outputs binary detection image.
- Displays detections
- Displays tags

logo spot detector