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-noise!

add-overlay-image

(add-overlay-image imp overlay x y opacity zero-transparent)
Add an overlay image into an image at a certain position.

add-overlay-image!

auto-threshold

(auto-threshold imp)
Automatically determine and threshold the imageplus.

auto-threshold!

autocontrast

(autocontrast imp)
Auto contrast. This is done the lazy way

autocontrast!

binary?

(binary? imp)
Is an imageplus binary?

blur-gaussian

(blur-gaussian imp sigma)
Gaussian blur on the currently imageplus/ROI.

blur-gaussian!

clear-all-images

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-stack-to-rgb!

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-binary!

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!

convolve-stack

(convolve-stack imp kernel kernel-width kernel-height)
Convolve a kernel with the whole stack.

convolve-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}})
Make a new image plus

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!

crop-stack

(crop-stack imp)
Crop the whole stack using the currently active ROI (bounding rectangle if non rectangle roi).

crop-stack!

dilate

(dilate imp)
Dilate the currently imageplus/ROI.

dilate!

draw-line

(draw-line imp x1 y1 x2 y2)
Draw a line on the imageplus from the 2 xy coords.

draw-line!

erode

(erode imp)
Erode the currently imageplus/ROI.

erode!

exp

(exp imp)
Exponential tranform on the imageplus/ROI

exp!

fill

(fill imp)
Fill the image/ROI with current fill value. This might not have the desirable ROI behaviors.

fill!

filter-imp

(filter-imp imp filter-type)
3x3 filter on imageplus, arguments are:
:blur-more, :find-edges, :median-filter, :min, :max

filter-imp!

find-edges

(find-edges imp)
Find edges in the imageplus/roi

find-edges!

flip-horizontal

(flip-horizontal imp)
Flip the imageplus horizontally.

flip-horizontal!

flip-vertical

(flip-vertical imp)
Flip the imageplus vertically.

flip-vertical!

gamma

(gamma imp val)
Gamma correction on the imageplus.

gamma!

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)
Return the string type.

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

(invert imp)
Invert an imageplus/roi

invert!

invert-lut

(invert-lut imp)
Invert the LUT of all processors in an ImagePlus' ImageStack.

invert-lut!

max-z-projection

(max-z-projection imp)
Return a max Z-projection. This is pretty dangerous because it uses window titles

median-filter

(median-filter imp)
3x3 median filter on an imageplus

median-filter!

open-image-sequence

(open-image-sequence directory)
Open an image sequence.

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!

put-pixel-double-unsafe

(put-pixel-double-unsafe imp x y val)
Put a pixel value at x,y of the imageplus.

put-pixel-double-unsafe!

put-pixel-int

(put-pixel-int imp x y val)
Put a pixel value at x,y of the imageplus.

put-pixel-int!

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.

put-pixel-int-unsafe!

reset-undo-buffer

(reset-undo-buffer imp)
Reset the undo buffer for an imageplus.

reset-undo-buffer!

resize-imp

(resize-imp imp width height)
Resize an image.

rotate

(rotate imp angle)
Rotate an imageplus by the supplied angle.

rotate!

rotate-left

(rotate-left imp)
Rotate an imageplus left by 90degrees.

rotate-left!

rotate-right

(rotate-right imp)
Rotate an imageplus right by 90degrees.

rotate-right!

save-imp

(save-imp imp filename)
Save an image.

save-imp-as-tiff

(save-imp-as-tiff imp filename)
Save an image as a tiff.

scalar-multiply

(scalar-multiply imp val)
Multiply every pixel of an imageplus by a value.

scalar-multiply!

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-background-value!

set-calibration

(set-calibration imp cal)
Set the calibration of an imageplus.

set-calibration!

set-fill-value

(set-fill-value imp val)
Set the default fill value for an imageplus.

set-fill-value!

set-histogram-range

(set-histogram-range imp hmin hmax)
Set the min/max of an imageplus' histogram.

set-histogram-range!

set-histogram-size

(set-histogram-size imp nbins)
Set the number of histogram bins for an imageplus.

set-histogram-size!

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-lut!

set-roi

(set-roi imp roi)
Set the roi of the imageplus to start-x start-y width height.

set-roi!

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)

set-voxel!

sharpen

(sharpen imp)
Sharpen an imageplus/roi with 3x3 kernel.

sharpen!

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.

size-filter-stack!

smooth

(smooth imp)
Smooth and image with 3x3 mean.

smooth!

split-channels

(split-channels imp)
Split channels.

split-rgb

(split-rgb imp)
Split an RGB type image.

split-stack

(split-stack imp)
Split an imagestack.

subtract-background

(subtract-background imp radius)
Perform 2D rolling ball subtraction.

subtract-background!

subtract-scalar

(subtract-scalar imp val)
Subtract a scalar from all pixels of an imageplus.

subtract-scalar!

threshold

(threshold imp thresh)
Threshold an imageplus with a supplied threshold.

threshold!

threshold-stack

(threshold-stack imp thresh)
Threshold the whole stack of an imageplus with a supplied threshold.

threshold-stack!

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.

update-imp!

watershed

(watershed imp)
Take the watershed of the current imageprocessor.

watershed!

watershed-stack

(watershed-stack imp)
Take the watershed of the current imageprocessor.

watershed-stack!

zconcat-imps

(zconcat-imps imps)
Concat a collection of imagepluses along the z-axis. (Might be weird with anything other than 2D images)