Spot detection | SciGet Microscopy Webapps

Input image

Drop a one-channel TIFF stack

Detection

Voxel z nm

Voxel yx nm iThe physical size of one voxel. It is read from ImageJ or OME-TIFF metadata when the file has it. The example's values are those of the Big-FISH tutorial: 300 nm between planes, 103 nm pixels.

Spot radius z nm

Spot radius yx nm iThe expected spot radius, roughly the PSF width. Divided by the voxel size it gives the LoG filter's sigma and the minimum distance between spots in voxels, as Big-FISH's get_object_radius_pixel does.

Detect in

Advanced settings

Threshold LoG response iLocal maxima of the filtered image above this value are spots. Leave it empty for Big-FISH's automatic threshold: the elbow of the curve of log spot count against threshold. The Analysis log gives the threshold each run used.

Sub-pixel Gaussian fit

Cell labels

Labels optional iAn integer label image, 0 for background and one value per cell, either one plane of the image's y × x size (applied to every z) or a stack of the image's size. Each spot counts in the cell under its voxel.

Output

Drop a TIFF stack anywhere, or choose an example.

Status Drag and drop files