fun.imagej.imp
add-noise
(add-noise imp std-dev)
Add noise to an imageplus with gaussian of mean 0 and the supplied std-dev.
add-overlay-image
(add-overlay-image imp overlay x y opacity zero-transparent)
Add an overlay image into an image at a certain position.
auto-threshold
(auto-threshold imp)
Automatically determine and threshold the imageplus.
autocontrast
(autocontrast imp)
Auto contrast. This is done the lazy way
blur-gaussian
(blur-gaussian imp sigma)
Gaussian blur on the currently imageplus/ROI.
close-all-images
(close-all-images)
Clear all images from ImageJ, including memory.
conj-imps
(conj-imps target-stack imp)
Conj an image to another image's stack.
convert-stack-to-rgb
(convert-stack-to-rgb imp)
Convert the stack to an RGB imageplus.
convert-to-16bit
(convert-to-16bit imp)
Convert an imageplus to 16 bit using the image stack.
convert-to-8bit
(convert-to-8bit imp)
Convert an imageplus to 8 bit using the image stack.
convert-to-binary
(convert-to-binary imp)
Convert an imageplus to 8 bit using the image stack.
convert-to-float
(convert-to-float imp)
Convert an imageplus to 32 bit using the image stack.
convert-to-RGB
(convert-to-RGB imp)
Convert an imageplus to 8 bit using the image stack.
convolve
(convolve imp kernel kernel-width kernel-height)
Convolve a kernel (kernel is a float array) with an imageplus.
convolve-stack
(convolve-stack imp kernel kernel-width kernel-height)
Convolve a kernel with the whole stack.
copy-calibration
(copy-calibration imp-a imp-b)
Copy the calibration from imp-a into imp-b
copy-imp
(copy-imp imp)
Return a duplicate of an image.
create-imp
(create-imp & {:keys [title type width height depth channels slices frames], :or {title "New ImagePlus", type "16-bit", width 512, height 512, channels 1, slices 1, frames 1}})
create-imp-like
(create-imp-like imp)
Create an ImagePlus like the input but blank.
create-lut
(create-lut imp)
Make a lookup table from an image.
crop
(crop imp)
Crop using the currently active ROI.
crop-stack
(crop-stack imp)
Crop the whole stack using the currently active ROI (bounding rectangle if non rectangle roi).
dilate
(dilate imp)
Dilate the currently imageplus/ROI.
draw-line
(draw-line imp x1 y1 x2 y2)
Draw a line on the imageplus from the 2 xy coords.
erode
(erode imp)
Erode the currently imageplus/ROI.
exp
(exp imp)
Exponential tranform on the imageplus/ROI
fill
(fill imp)
Fill the image/ROI with current fill value. This might not have the desirable ROI behaviors.
filter-imp
(filter-imp imp filter-type)
3x3 filter on imageplus, arguments are:
:blur-more, :find-edges, :median-filter, :min, :max
find-edges
(find-edges imp)
Find edges in the imageplus/roi
flip-horizontal
(flip-horizontal imp)
Flip the imageplus horizontally.
flip-vertical
(flip-vertical imp)
Flip the imageplus vertically.
gamma
(gamma imp val)
Gamma correction on the imageplus.
get-auto-threshold
(get-auto-threshold imp)
Get the value that would be used by auto threshold.
get-background-value
(get-background-value imp)
Return the current background fill value.
get-bit-depth
(get-bit-depth imp)
Return the bit depth of an imageplus.
get-calibration
(get-calibration imp)
Return the calibration of an imageplus.
get-current-imp
(get-current-imp)
Return the currently open ImagePlus.
get-fileinfo
(get-fileinfo imp)
Return the fileinfo for an ImagePlus
get-filename
(get-filename imp)
Return the filename of an imageplus if it exists.
get-height
(get-height imp)
Return the height of an image.
get-histogram
(get-histogram imp)
Return the histogram of the imageplus/ROI.
get-histogram-max
(get-histogram-max imp)
Return the maximum value for the image (for float imagepluses).
get-histogram-min
(get-histogram-min imp)
Return the minimum value for the image (for float imagepluses).
get-histogram-size
(get-histogram-size imp)
Return the number of bins of a histogram (for float imagepluses).
get-imp-type
(get-imp-type imp)
Return the type of an ImagePlus.
get-line
(get-line imp x1 y1 x2 y2)
Return an array of pixels along the line within the imageplus.
get-max
(get-max imp)
Return the maximum value in an imageplus.
get-min
(get-min imp)
Return the minimum value in an imageplus.
get-num-channels
(get-num-channels imp)
Return the number of channels in an ImagePlus.
get-num-dimensions
(get-num-dimensions imp)
Return the number of dimensions in an ImagePlus.
get-num-frames
(get-num-frames imp)
Return the number of frames in an ImagePlus.
get-num-slices
(get-num-slices imp)
Return the number of slices in an ImagePlus.
get-numeric-property
(get-numeric-property imp propkey)
Return a numberic property from the info property string.
get-pixel
(get-pixel imp x y)
Return the pixel value at x,y (this does bounds checking and is slower, for a faster op check get-pixel-unsafe)
get-pixel-float
(get-pixel-float imp x y)
Return a pixel's value as a float.
get-pixel-unsafe
(get-pixel-unsafe imp x y)
Get pixel without bounds checking (faster)
get-roi
(get-roi imp)
Returns the roi of an imp.
get-stack-depth
(get-stack-depth imp)
Return the depth of the image stack.
get-title
(get-title imp)
Return the title of an ImagePlus.
get-type-string
(get-type-string imp)
get-voxel
(get-voxel imp x y z)
Return the voxel value of an imageplus (assuming it is an imagestack)
get-width
(get-width imp)
Return the width of an image.
grayscale?
(grayscale? imp)
Is an imageplus grayscale?
imp-dimensions
(imp-dimensions imp)
Return the dimensions of an image.
imp-flatten
(imp-flatten imp)
Flatten the overlay of an imageplus.
imp-from-clipboard
(imp-from-clipboard)
Return the imageplus in theclipboard.
imp-from-processor
(imp-from-processor ip title)
Make an image plus from an imageprocessor.
imp-from-stack
(imp-from-stack stack title)
Make an image plus from an imagestack.
imps-to-rgb
(imps-to-rgb imps & args)
Convert a sequence of imps (only first 3 or fewer if less supplied) to RGB.
invert-lut
(invert-lut imp)
Invert the LUT of all processors in an ImagePlus' ImageStack.
max-z-projection
(max-z-projection imp)
Return a max Z-projection. This is pretty dangerous because it uses window titles
open-image-sequence
(open-image-sequence directory)
open-imp
(open-imp filename)
Open an image using bioformats, this returns an array of imageplus's. Return the first, see open-imps to open many imagepluses at once
open-imps
(open-imps filename)
Open an image using bioformats, this returns an array of imageplus's
put-pixel-double
(put-pixel-double imp x y val)
Put a pixel value at x,y of the imageplus.
put-pixel-double-unsafe
(put-pixel-double-unsafe imp x y val)
Put a pixel value at x,y of the imageplus.
put-pixel-int
(put-pixel-int imp x y val)
Put a pixel value at x,y of the imageplus.
put-pixel-int-unsafe
(put-pixel-int-unsafe imp x y val)
Put a pixel value at x,y of an imageplus without bounds checking.
reset-undo-buffer
(reset-undo-buffer imp)
Reset the undo buffer for an imageplus.
resize-imp
(resize-imp imp width height)
rotate
(rotate imp angle)
Rotate an imageplus by the supplied angle.
rotate-left
(rotate-left imp)
Rotate an imageplus left by 90degrees.
rotate-right
(rotate-right imp)
Rotate an imageplus right by 90degrees.
save-imp
(save-imp imp filename)
save-imp-as-tiff
(save-imp-as-tiff imp filename)
scalar-multiply
(scalar-multiply imp val)
Multiply every pixel of an imageplus by a value.
seq-to-imp
(seq-to-imp width height depth coll)
Make an image from a sequence. Depth is ignored.
set-background-value
(set-background-value imp val)
Set the background fill value of an imageplus.
set-calibration
(set-calibration imp cal)
Set the calibration of an imageplus.
set-fill-value
(set-fill-value imp val)
Set the default fill value for an imageplus.
set-histogram-range
(set-histogram-range imp hmin hmax)
Set the min/max of an imageplus' histogram.
set-histogram-size
(set-histogram-size imp nbins)
Set the number of histogram bins for an imageplus.
set-interpolation-method
(set-interpolation-method imp method)
Set the interpolation method of the current processor of an imageplus.
set-lut
(set-lut imp lut)
Set the lookup table (LUT) for color coding this image.
set-roi
(set-roi imp roi)
Set the roi of the imageplus to start-x start-y width height.
set-title
(set-title imp title)
Set the title of an imageplus.
set-voxel
(set-voxel imp x y z val)
Set the value of a voxel of an image plus (assuming it is an imagestack)
sharpen
(sharpen imp)
Sharpen an imageplus/roi with 3x3 kernel.
show-imp
(show-imp imp)
Display an image, expects an ImagePlus.
size-filter-stack
(size-filter-stack imp & args)
Size filter an image slice by slice over the whole stack.
smooth
(smooth imp)
Smooth and image with 3x3 mean.
split-channels
(split-channels imp)
split-stack
(split-stack imp)
subtract-background
(subtract-background imp radius)
Perform 2D rolling ball subtraction.
subtract-scalar
(subtract-scalar imp val)
Subtract a scalar from all pixels of an imageplus.
threshold
(threshold imp thresh)
Threshold an imageplus with a supplied threshold.
threshold-stack
(threshold-stack imp thresh)
Threshold the whole stack of an imageplus with a supplied threshold.
tile-imps
(tile-imps imps)
(tile-imps imps width height)
Tile a set of images, currently assumes all are same size as the first one.
update-imp
(update-imp imp)
Update the display of an imp.
watershed
(watershed imp)
Take the watershed of the current imageprocessor.
watershed-stack
(watershed-stack imp)
Take the watershed of the current imageprocessor.
zconcat-imps
(zconcat-imps imps)
Concat a collection of imagepluses along the z-axis. (Might be weird with anything other than 2D images)