Count nuclear or cellular foci

Parameters:

Name	#	Type	Description
Number of labels to measure (1-3)	1	integer	Select how many label channels tom measure. Each channel can be selected multiple times.
Histogram or distribution calculation	2	string	Select Histogram to show output as histogram, or None to show individual cell values.
Channel Number, nuclear stain	3	integer	Channel number of the nuclear marker used for segmentation. Intnesities are not measured here.
Morphological parameter measurement for nuclei	4	string	Plots and saves time course of selected morphological data
Foci: Channel Number, label #1	5	integer	Channel number of label #1 to be measured. Each channel can be selected multiple times for different measurements.
Foci: Background subtraction method	6	string	Select background subtraction method: Percentile, Rolling ball, Spatial filtering, None. See settings below. Background subtraction is performed in the same way for all channels.
Foci: Count foci over	7	string	Intensity measurement is performed either over the nucleus or in a perinuclear ring.
Foci: Perinuclear ring width (pixels), label #1	8	integer	Width of the ring around the nucleus to measure perinuclear area, in pixels. This is used only if "Perinuclear ring" is selected above.
Foci: Positive control reference image operation	9	string	The positive control is an image with many visible foci. Using a positive control avoids amplifying background noise in samples with little or no foci. Alternatively enter fixed threshold value here.
Foci: Sensitivity (0-1, less is more sensitive) or threshold	10	real	Sensitivity factor for Otsu's threshold determination. Smaller value will result a smaller threshold for foci brightness compared to local background.
Foci: maximum size (area, pixels)	11	integer	Maximal size of object counted as foci (pixel area).
#2: Channel Number, label #2	12	integer	Channel number of label #2 to be measured. Each channel can be selected multiple times for different measurements.
#2: Measure label #2 fluorescence over	13	string	Intensity measurement is performed either over the nucleus or in a perinuclear ring.
#2: Intensity measurement type of label #2	14	string	Available plot types: "Mean", "Sum", "Variance", "PDI variance", "PDI sd", "Line Scan". These statistics describe pixels within each segment. To calculate statistics between segments use the "Mean of all traces" option.
#2: Perinuclear ring width (pixels), label #2	15	integer	Width of the ring around the nucleus to measure perinuclear area, in pixels. This is used only if "Perinuclear ring" is selected above.
#3: Channel Number, label #3	16	integer	Channel number of label #3 to be measured. Each channel can be selected multiple times for different measurements.
#3: Measure label #3 fluorescence over	17	string	Intensity measurement is performed either over the nucleus or in a perinuclear ring.
#3: Intensity measurement type of label #3	18	string	Available plot types: "Mean", "Sum", "Variance", "PDI variance", "PDI sd", "Line Scan". These statistics describe pixels within each segment. To calculate statistics between segments use the "Mean of all traces" option.
#3: Perinuclear ring width (pixels), label #3	19	integer	Width of the ring around the nucleus to measure perinuclear area, in pixels. This is used only if "Perinuclear ring" is selected above.
Histogram: number of bins	20	integer	When the output is histogram, the histogram is calculated using this number of equal sized bins, where the lowest bin starts at the smallest data point and the highest bin ends at the largest data point. If explicit range definition is used below, the bins will bound the given range. Use zero bin size for automatic binning.
Positive control reference image operation for nuclei detection	21	string	The positive control is an image with many visible cells. Using a positive control avoids amplifying background noise in wells with little or no cells.
Suppress debris and outside of well areas	22	boolean	Brighter areas corresponding to the bottom of microplate outside the well area will be masked.
Debris masking: minimum diameter of continuous bright spot	23	real	Farthest points of the maximal cross section. 0 for not checking
Debris and well edge detection sensitivity (%)	24	real	Pixel value, percentile, or factor times Otsu optimal threshold value (typically 1)
Cells: Nucleus diameter (pixels)	25	integer	Diameter of the nucleus in pixels. Nuclei ranging around this size will be selected.
Cells: Debris cutoff for ICC and nuclear stain (percentile)	26	real	This percentile of the image histogram sets the intensity value where the maximum of the Look Up Table (LUT) is scaled. Use -1 to override this with fixed value set below at "Max value".
Cells: Minimum cell fluorescence (%)	27	real	Cells dimmer than this in filtered rescaled TMRM+FLIPR projection images will be rejected. Increase this value if debris dimmer than the cells is detected.
Cells: Shape factor (minimum; 0-1)	28	real	1 for disc, smaller for irregular shapes. 0 for not checking
Cells: Weld segments into round objects	29	boolean	Weld touching segments if they form a rounder object together. Use this to avoid objects fragmenting into multiple segments.
Cells: Discard segments at edges of the image	30	boolean	Any segment that has at least 10% of its boundary at the edge of the image will be discarded.
Background subtraction method	31	string	Select background subtraction method: Percentile, Rolling ball, Spatial filtering, None. See settings below. Background subtraction is performed in the same way for all channels.
Background percentile	32	real	If background subtraction method is percentile, this percentile value will be used in all channels.
Local background: Rolling ball: median filter size	33	integer	The median is calculated over a width x width rectangular area around each pixel of the image.
Local background: Spatial filtering: Number of tiles in x	34	integer	The image consists of this number of equal sized tiles in x dimension.
Local background: Spatial filtering: Number of tiles in y	35	integer	The image consists of this number of equal sized tiles in y dimension.
Local background: Spatial filtering: Largest object size (for background removal, pixels times number of tiles)	36	real	Size of the object to be passed by the filtering. The pixel size must be multiplied by the number if tiles (in x or y). Objects larger than this will be removed as background. Cut on of the band pass Butterworth filter.

Description:

This pipeline counts bright foci in nuclei or in perinuclear area and measure fluorescence intensities over nuclei or perinuclear areas using a nuclear marker and 1-3 label channels. Use the "Count cellular foci with secondary cell segmentation" pipeline instead if foci in the cell rather than in the nucleus are to be counted, and a whole cell label has been imaged. The pipeline can run in single or tiled images and in whole wells with automatic suppression of outside of the well areas and debris (see “Suppress debris and outside of well areas”). Different measurements may be done in the same label channel. One channel is used for foci count and 0-2 channels for intensity measurements. Multiple background subtraction options are uniformly applied to all intensity channels, and can be separately specified for the foci count.

Sample: fixed or live cells stained for nuclei e.g. with Hoechst 33342 or DAPI, and showing other fluorescence of interest.

Input: 2-4 channels fluorescence image showing a nuclear marker (e.g. Hoechst 33342 or DAPI) and immuno- or other fluorescence visible over the nuclei or in perinuclear areas. Medium or high magnification (40x or above).

Output: 1 morphological parameter of choice of nuclei, the count of foci per nucleus (or cell) and 0-2 optional intensity measurements in the same or different label channels measured over nuceli or perinuclear area. For intensity measurement the “Intensity measurement type of label #” statistics (Mean, Sum, Variance, Punctate over diffuse ratio) is calculated over nuclei or perinuclear area see (“Measure label # fluorescence over” and “Perinuclear ring width”). Output data are single cell values or histogram (see “Histogram or distribution calculation”). Note that the order of labels measured in the output worksheet may vary due to parallel processing.

Reference image operation: by default, the calculation of nuclei is self-referenced. Thus, it is independently calculated for each image. There are two separate reference image options, one for the nucleus counting and one or the foci counting. This is set by the “Positive control reference image operation for nuclei detection” = ”Self-referenced” option. This works well if none of the samples have very few cells (foci) compared to others. If cell density varies between samples, or if some samples have very few cells (foci), use positive control reference. The positive control is one of the images from the data set with about maximum number of cells and positive cells. To make reference image set “Positive control reference image operation for nuclei detection” = ”Make reference image”. Process a positive control sample. The reference images will be minimized, and reused at the following operations. Then set “Positive control reference image operation for nuclei detection” = ”Use reference image” and process all data. The foci detection alternatively allows a fixed threshold that is a pixel intensity for the peak brightness of foci compared to the local background.

Debris avoidance: to increase sensitivity, increase “Large debris removal sensitivity (%)” and decrease “Large debris minimum size (length in pixels)”. To decrease sensitivity, do the opposite. Debris avoidance may avoid cells or positive cells, if the cell count or positive cell count is too low. In this case set a small (non-zero) %, e.g. 1 as sensitivity.

Background subtraction:
Choose percentile-based global or local background subtraction methods. For tiled images: the background tiling pattern or vignetting is efficiently removed by spatial filtering if the recording was performed without overlap and image registration. Provide the number of tiles in x and y direction in the “Local background: Spatial filtering: Number of tiles in x” and “…y” parameters.

Adjustments:
Set approximate cell diameter. To this end load an image, zoom in using the magnifier glass Main Toolbar button, and then using the linear ROI button draw a line across a nucleus. Double-click the status bar of the Image Window to see the length of the ROI (Size of active ROI).
Run the pipeline on a single well and observe the results. In the overlay Image Window the gray fluorescence image should be well matched by the colored segments:
*If single nuclei are detected as multiple segments, increase the approximate cell diameter. In addition, you may turn segment welding on.
*If multiple nuclei are detected as single segments, decrease the approximate cell diameter. In addition, you may turn segment welding off.
*If debris is detected a nuclei, increase background cutoff or minimum cell fluorescence.
*If dimmer cells are missed, decrease background cutoff or minimum cell fluorescence.
*If bright debris outshines cells, decrease debris cutoff percentile.
*if too few of the foci are detected, decrease the threshold in “Foci: Sensitivity (0-1, less is more sensitive) or threshold” and may increase the “Foci: maximum size (area, pixels)”.
*if too many foci are detected, increase the threshold in “Foci: Sensitivity (0-1, less is more sensitive) or threshold” and may decrease the “Foci: maximum size (area, pixels)”.

If segmentation goes as it is desired, process the whole microplate using the double blue arrowhead button and ‘Run Pipeline … on All Stage Positions’.

V1: based on “Fluorescence and absorbance histometry using nuclear and secondary whole cell segmentation (1-4 labels - advanced background options)”.