Image Tools

Background

This package is presented as a way for users to load, display, and print out summary views from sets of TIFF images or internally-existing xy/image waves without needing to write code.

Operation

Once installed, the package is accessible from the Packages->Panels->Image Tools menu.

The displayed content is divided as four frames.

  • An image display window shows the currently active image
  • A control bar on the top of the main display sets the parameters in the viewing window
  • A histogram graph shows the histograms for the image being displayed.
  • Operation of the package is done using inputs on a control panel.

Image Control Bar

  • Split view to show threshold or background side-by-side to image
  • Change the image range (contrast adjustments), invert, or show as black & white
  • Change the color scale used to display the image

Main Tab

Image Display
  • Step through images that are loaded as sets using buttons to advance or go backward in the loaded sets.
  • See the image size (pixels) and bit depth.
  • View/Add notes to an image file (wave).
  • Play a movie of a stack
Marquee
  • Shows the positions of the marquee when drawn on the image
Information Display
  • Toggle on/off the histogram on linear and log scales as well as the cumulative and derivative histograms.
  • Scale the derivative histogram to search for positions of zero crossings (peaks in histogram).
  • Select a region of interest (RoI) to show the histograms.
  • Choose inside, outside, inside - outside, and outside - inside analysis for histogram
  • See where the RoI is in image coordinates.
  • Lock the RoI to continue using the selection tool on the image.

Load Tab

Load TIFF(s)
  • Load a single image, multiple images, a folder of images, or a selection of images from a stack.
  • Load a stack or multiple files as a stack.
  • Load / Convert existing xy waves to a format that can be used within the package
  • Choose to keep the source (or not), to extract any one or all of the RGB channels, and/or to create a grayscale image.

Calibrate Tab

Calibrate XY
  • Set a calibration factor for pixel, image width, or image height to apply locally or globally.
Remove Background
  • Select or edit points that denote the background locations
  • Apply the operation to remove a background

Process Tab

Threshold
  • Apply a thresholding method to one image, each image, or all images in a stack.

Print Tab

Image Layout
  • Turn on/off axes
  • Turn on/off scale bar and set its location / color
Contact Print
  • Store the image to a list to use for a contact print

Caveats

  • This version has only been tested with single-layer images. The ability to handle RGB images properly has yet to be developed. Convert RGB to grayscale or read only the individual channels accordingly.
  • This program can load image stacks (TIFF movies). That does not however mean that it will handle them all with equal efficiency. Load larger files as stacks using the selections to load only a certain range in the movie and/or to load only a certain sequence (e.g. every 10th image).

Future Plans

Plug-in architectures for other developers.

Images:

Image Tools v2.40 Image

Project Details

Current Project Release

Release File: Image Tools v242.zip
Version: 2.42
Version Date: Fri, 04/06/2018 - 03:11 pm
Version Major: 2
Version Extra: 42
OS Compatibility: Windows Mac-Intel
Release Notes:

Squashed Bugs

  • fixed an error to load a folder as individual files
  • fixed an error in removing background on all images in stack
  • fixed a mistake where the plane number on the display could exceed the number of layers in the stack

Added Features

  • prints reports about settings for background and threshold operations to a notebook

Improved Code / UI

  • reports properly to history whether the package is newly started or restarting
  • background removal algorithm consistent regardless of individual image, single plane, or entire stack
  • improved the approach to select an image to show in a split
View All Releases

I would be grateful to hear from folks who find this package useful, who would like to see features added to it, or who would like to contribute to its development. Please contact me with comments here or via a direct email.

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