The MiCA application offers basic functionality to analyse 2D fluorescense microscopy images of cells. Features:
algorithms for cell boundary detection based on active contours
methods for sub-cellular structure detection based on wavelets
integrated statistical analysis of segmentation results like counts of structures per cell or other statistical numbers
visual and tabular result data presentation
Input image
the multi-channel image to be analyzed
Nucleus channel
index of image channel with labeled nuclei
the channel index starts with 1
if the channel index is set to -1, nuclei detection is disabled
Cytoplasm channel
the channel of the image to use for cell cytoplasm segmentation
the channel index starts with 1
if the channel index is set to -1, cytoplasm detection is disabled
Nuclei detector
operator to be used for nuclei detection, for details refer to the documentation about Nucleus Detection in MiToBo
Nuclei contours
if a channel index for nuclei detection is specified as required parameter this parameter is ignored
otherwise you can specify nuclei contours here
to load contours use one of the following modes:
ROI MANAGER: requires selections in the ImageJ ROI Manager
MTB XML: read file with contours saved in MiToBo XML format
SERIAL XML - not fully supported yet
MANUAL: manually enter contours by specifying list of points
pressing the "Load" button will import the selected contours.
Cytoplasm detector
operator to be used for detecting the cell cytoplasm, for details refer to the documentation about Cytoplasm Detection in MiToBo
Apply Gauss to cytoplasm channel
enables/disables optional Gaussian smoothing of the channel for cytoplasm segmentation prior to the actual segmentation
Gauss sigma
the standard deviation to be used for Gaussian smoothing
if Gaussian smoothing is disabled the parameter is ignored
Particle Detector
operator to be used for particle detection, for details refer to the documentation about Particle Detection in MiToBo
Measurement Units
currently not used
Show final result image stack
disables/enables the display of a stack with all segmentation results, i.e. nuclei and particle masks as well as cell cytoplasm contours
Show intermediate results
disables/enables display of intermediate results during operator execution
Save intermediate results
disables/enables the saving of intermediate results to disk
Save intermediate results to...
path where to save intermediate results
Show b/w masks
enables display of binary masks
if disabled colored overlays of the segmentation results are shown
List of channel IDs to copy to result
allows to specfiy a list of channel indices for copying related channels to the result stack (ignored if stack option is disabled)
Verbose
disables/enables output of additional messages on console