ImageJ notes & macros

General information (mine and others)

• getting_started/ A guide to foolproof installation.
• Instructions how to use ImageJ. https://imagej.nih.gov/ij/docs/menus/image.html
• Excellent overview for beginners at https://nif.hms.harvard.edu/sites/nif.hms.harvard.edu/files/education-files/Fiji%20for%20Beginners.pdf (except I still prefer ImageJ to Fiji)
• fft/
• Composite Colors & using Hyperstacks
• intensity primer
• Example of how we misperceive relative intensities and need computers to do the measurements
• CLAHE a.k.a. Local Contrast
• About the annulus intensity method

Macros and utilities (mine and others)

• Useful Collection of Macros (replaces Dustin_lab_ND2_macros_v108_last_version_before_adding_hyperstacks)
• Selective Z projections
• Simple way to make figures from multichannel images.
• Assign colors to multichannel images
• Merge pairs of green and red grayscale files that were saved separately. Operates on all pairs in a directory.
• MultiChannel_Conversion_to_8bit_Macros
• 3D rendering
• tool to 3D_project_from_current_slice_up
• Straighten function in ImageJ
• Shortest distance to perimeter of a feature a.k.a. Ship to Shore
• Metadata and putting on images or using as test conditions.
• Process sequences of files in nested directories within directories that have fixed directory names.
• Make_All_Images_In_Folder_8bits_v101 is useful for a folder full of tif files that may be 12, 14, 16, or 32 bits. It also may be used as a template for writing other batch processing macros with an example of getting info from the user too.
• Convert all ND2 files in a folder to TIF with a few options for enhancement, montaging, etc.
• Return the mean intensity of the brightest n pixels of ROIs through a Z or T series. This is an earlier version measuring intensity through time.
• measure_Zstack_intensity/
• xy_cell_profiler/
• montaging stacks
• Measure_Volumes_and_Intensities_v102_for_Zeiss510_images (originally for Anastasia)
• Plot profile multiple channels
• This modification of Useful Collection 20180529 has snipstack [F4] changed to rotate each ROI based on angle of best fitting ellipse. Written for aligning bacteria in a stack of many fields of view.
  
• Dustin_lab_ND2_macros_for_hyperstacks_v114
• Benfords_distribution_v103 as a test for randomness (expected results). This version gets rid of the zero digit.
• Process_and_Save_all_LSM_files_in_a_directory_v101
• make a grid pattern of spots
• Local Linear Contrast Enhance
• Median Filtering
• 4X6 resizer (or resize to any fixed aspect ratio)
• A web page for counting colonies and an earlier method for Counting Bacterial or Yeast Colonies -- Example images 01 and 02
• Colocalization tools (in progress...) and JACOP_on_a_whole_directory_v101a
• Colocalization simulation and real measurement - also a warning about analyzing a maximum projection image
• mark_center_of_ROI_v100
• Save ROI Manager in Image Directory
• Manually extract frames from a hyperstack and put in a new stack
• LUTs (Look Up Tables)
• Radial plots, angle vs. distance and times color coded
• Radial reslicing
• Shortest distance between all pairs of points & clustering - analysis method looking for an application
• Integrated intensity function for packaging in other macros
  New implementation 20151115 simplified.
• integrated_intensity_at_incrementing_thresholds
• Complement to cell counter, click to count clusters marked with convex hull outline.
• Save Leica LIF files as individually named files with shortened filenames
• Example of measuring multiple channels multiple images
• Extract slices from a hyperstack and pop onto a new stack - corrects focus shifts
• Float the stack
• Draw concentric circles on image. Circles are nondestructive overlay.
• first iteration of Puncta Counting Macros
• Mark location found on plot profile curve on original image
• Measure width of an object
• Cut a region of interest into equal parts
• Capture Slidepath or other screen image and prompt user to do meaurements.
• StackReg and Image registration or alignment.
• Interactive slope of line and examples of live running macros and "is" command.
• tables example code in ImageJ (also see https://imagej.nih.gov/ij/developer/macro/functions.html#T)

Drawing or simulating with ImageJ:

• simulation_microclusters_moving_to_center_v101 and example result [PNG]
• simulation of particles moving to test particle tracking software with known values Version01; Version02; Version02
• And more...

Instructions from other sources:

• Main ImageJ Documentation page,
  ImageJ Basics (originally from http://rsb.info.nih.gov/ij/docs/pdfs/)
  ImageJ User Guide Online
  or as PDF version 1.46r
• Wright Cell Imaging Facility ImageJ manual
• ImageJ Wiki
• FIJI version of ImageJ including tutorials
• Want to write Java plugins instead of slower macros? https://albert.rierol.net/imagej_programming_tutorials.html#ImageJ%20programming%20basics
• and do your own Google/Bing search for more
• Custom filters for Photoshop (and ImageJ) that look really interesting.
• I have not vetted this web page, but I expect is it good: https://www.bwhneurosciences.org/neurotechnology-studio/training-resources/

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comments, questions, suggestions: mcammer@gmail.com