Hello Richard,
I'm not sure what your sample looks like, but if you're working with
bacteria (around 0.6 µm by 3-4 µm, though it might be different in your
case), the so-called 'clumps' could be groups of bacteria. I would
suggest comparing the fluorescence intensity between the 'clumps' and
the surrounding areas of lower intensity. If the difference in intensity
is significant, and you're using widefield imaging, you may notice a
halo effect around the clumps that you might want to remove.
If possible, the best approach would be to modify the sample preparation
to prevent clump formation. Otherwise, you could segment the
high-intensity areas that you identify as 'clumps', create a region of
interest (ROI) list, and then apply an appropriate intensity level
within those ROIs. When segmenting, beware of your intensity cutoff
value set to binarize your original image.
I hope this helps!
Javier
F Javier Diez-Guerra, PhD
Servicio de Microscopía Óptica Avanzada (SMOA)
Centro de Biologia Molecular Severo Ochoa
C/ Nicolás Cabrera, 1
Campus de Cantoblanco
28049 Madrid
SPAIN
Tel +34 91 196 4612
e-mail: [email protected]
On 24/01/2025 15:38, Cole, Richard W (HEALTH) wrote:
I have a user working with bacteria (fluorescently labeled). I need to remove
clumps with very high-intensity values, and I am looking for a way to retain
the lower intensities.
Any ideas would be greatly appreciated.
Richard Cole
Research Scientist V
Director: Advanced Light Microscopy & Image Analysis Core RRID:SCR_021104
New York State Dept. of Health Wadsworth Center
120 New Scotland Avenue, Albany, N.Y. 12208
518-474-7048 Phone
518-408-1730 Fax
Sponsored program officer-Association of Biomolecular Resource Facilities
(ABRF.org)
Research Associate Professor
Dept. of Biomedical Sciences
School of Public Health State University of New York
orcid.org/0000-0002-3161-8319
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