Fiji Cell Counter
Fiji Cell Counter - Related Videos
09:33
Determining Cell Number During Cell Culture using the Scepter Cell Counter
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Cited by 56 •
2010
The Scepter Cell Counter is a handheld automated device that can be used to count cells, monitor cell diameter and volume, and be used to check the health and quality of cellular populations from one culture to the next.
10:09
EasyFiji: A Graphical Interface for User-Friendly Fluorescence Image Processing in Fiji
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2026
EasyFiji is a graphical user interface plugin for Fiji (ImageJ) that provides a curated suite of fluorescence image visualization and processing tools frequently utilized by life scientists.
13:16
Determination of Mammalian Cell Counts, Cell Size and Cell Health Using the Moxi Z Mini Automated Cell Counter
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Cited by 18 •
2012
The Moxi Z miniature automated cell counter is a novel instrument that combines the Coulter Principle with patented thin-film sensor technology and a proprietary software algorithm to perform sizing and counting of a broad size range of particles as well as to determine the overall health of monodisperse mammalian cell cultures. This protocol describes the use of this instrument for counting and assessing the health of cell cultures.
07:31
Agarose-Based Model Ecosystem for Cultivating Methanotrophs in a Methane-Oxygen Counter Gradient
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2024
A protocol is described for preparing a simple model ecosystem that recreates the methane-oxygen counter gradient found in the natural habitat of aerobic methane-oxidizing bacteria, enabling the study of their physiology in a spatially resolved context. Modifications to common biochemical assays for use with the agarose-based model ecosystem are also described.
08:57
Quantification of Optic Nerve Cross Sectional Area on MRI: A Novel Protocol using Fiji Software
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2021
We provided a detailed protocol for a standardized method of optic nerve assessment and quantification using MRI, utilizing a widely available imaging sequence, and open access software for image analysis. Following this standardized protocol would provide meaningful data for comparison between different patients and different studies.
FAQs
Numbered overlays provide a visible record of counting progress directly on the microscopy image. As each cell or feature is clicked, Fiji assigns a marker number and retains it on the display. The counter also separates tallies by marker type, helping users identify which structures have already been counted and reducing the risk of duplicate measurements.
Marker types let a single image support more than one counting category. Instead of treating every click as an undifferentiated total, the user can select a marker associated with the structure being recorded and then click the relevant cells or features. Fiji maintains counts for those marker types, organizing measurements when images contain distinct populations or marked structures.
Manual counts can provide a human-reviewed basis for developing or evaluating automated image-analysis methods. By marking cells directly in microscopy images, a researcher produces inspectable locations and recorded numerical totals. These results connect visual review with automated workflows, supporting training and validation while keeping the counted structures visible for comparison.
A basic workflow starts by opening the microscopy image in Fiji and choosing the counting marker or markers required for the analysis. The user then clicks each target cell or feature, while the plugin records the selected marker type and places numbered overlays on the image. The displayed markers help confirm that intended structures were counted once.
Counts can be used to examine changes in cell populations, tissue organization, or proliferation across developmental stages. Applying the counting workflow to experimentally generated microscopy images links stage-specific visual observations to numerical results. This allows developmental patterns apparent in tissue images to be represented as count-based measurements rather than remaining solely qualitative descriptions.
The tool is useful when researchers need a straightforward visual way to convert experimentally generated microscopy images into numerical data. It can support biological quantification, provide training in image-based counting, and help validate automated methods. Because numbered markers remain visible during analysis, the counting process can also be inspected while measurements are being produced.