BlobFinder can perform two types of analysis; an average count and a single cell analysis. The average count analysis will count the number of fluorescent signals and nuclei in an image. The output is a txt-file, importable to e.g. excel, showing the number of signals and nuclei in each image.
A heterogeneous cell population contains cells that differ in some way, and if using the average analysis these differences can not be seen. To quantify differences among the cells in the same image the single cell analysis should be used. This analysis simulates a cytoplasm and assigns each signal to a particular cell. In the output every cell has a value representing the number of signals in that particular cell.
The software can also work on z-stacks of the cells by using a maximum projection to project the image data into a 2D image. Each slice is filtered by a signal enhancing filter before projection.
Output from average analysis
· Number of signals in the image
· An intensity measure of the signals
· Number of nuclei in the image
· A TIF image showing the outline of each nucleus and a marker of each signal overlaid on the original image (projection if 3D).
Output from single cell analysis
· An ID for every cell
· Number of signals for each cell
· An intensity measure of the signals for each cell
· Area of nuclei and cytoplasm for each cell
· A TIF image showing the outline of each nucleus and cytoplasm together with the ID number for each cell as well as a marker for each signal overlaid on the original image (projection if 3D).
Import to analysis
· The import to the analysis is TIF images structured as an export from a Zeiss microscope,
More info on the import format of the images can be found in the help section and in the help menu in the software
May 4th 2009 (Blobfinder BrighField beta available for download)
A new version of BlobFinder for Brightfield images is available in the download section.
February 20th 2009 (BlobFinder paper published)
A. Allalou, C. Wählby, BlobFinder, a tool for fluorescence microscopy image cytometry, Computer Methods and Programs in Biomedicine, 94(1);58-65, 2009. Link
November 11th 2008 (BlobFinder V3.2)
A new version of BlobFinder has been made available in the download section.
September 2nd 2008 (BlobFinder V3.1beta)
A new an improved version of BlobFinder has been made available in the download section.
August 20th 2008
BlobFinder; a tool for fluorescence microscopy image cytometry has been accepted for publication in the journal Computer Methods and Programs in Biomedicine.