Plugins and Macros
Group Plugins in Emory ICI folder to keep things neat
Create a new folder "Emory ICI" in your plugins folder of your ImageJ/Fiji software. Place each of the plugins you need into this folder and they'll appear under Emory ICI in the plugins menu. Email neil.anthony@emory.edu with questions and/or requests for updates/changes.
Convert to .ome.tif Macro
Full ImageJ 1.x macro to acompmany the 4 part YouTube mini series on OME Tiff files: convert-to-ome.ijm
Part 1 - Simple Export: https://youtu.be/WjDfgKDlWrI
Part 2 - Metadata: https://youtu.be/JJMw61EAEWM
Part 3 - Macro: https://youtu.be/abJMLARuNvY
Part 4 - Tidy Macro: https://youtu.be/5-fBu_tJDRQ
Olympus to Fiji Stitch Converter
Convert MATL log files from Olympus Fluoview software into text files for use with Fiji's stitching plugin.
Olympus .vsi File Inspection
Generate report of folder containing .vsi files. Reports image filename, number of images in file, boolean list of which sub-images have metadata, and a list of file sizes. Save report as .csv file and open in Excel. If certain files produce errors or contain vastly different numbers of sub-images (called series in Fiji) check the number of subfolders in the data folder sharing the same name as the vsi file. Move additional subfolders to temp location and rescan.
Olympus .vsi File Conversion
Use below macro (right click and Save As... and then drag onto Fiji) to convert specified sub-image/series within vsi file to tif (also saves png thumbnail for easy viewing). Select common size from above report, using the series number counted along the columns. Note, the first sizes listed prior to the largest are commonly image files, not data files.
Cellular Edge Profile Plugin
Creates straightened profile along the center of thresholded band (intended for periphery of cell body). Select channel (if multi-channel.composite image) and use sliders to adjust location of the band and click Profile to create the straightened image.
Sliders perform as follows:
Lower Threshold: Starting point intensity of outer part of band.
Thickness: Thickness of band in pixels.
Offset: Offset of band in pixels.
Edge %: Adjusts how the image edges are used for the threshold boundary. Higher percentages will allow the band to follow signal touching the edges, and lower percentages will block the theshold and create a straight boundary at the image edge.
Notes:
- The displayed band is created with erode and dilate function, and can look a little rough, but the straighten profile is a curved line fitted to the approx center of the band with a thickness set in the slider.
- The result includes all channels, has a data type of 32bit floating point (i.e. with decimal places), and will likely include dark regions where the threshold hits the image edges.
- The Profile created grabs the largest region if multiple regions are present.
- Only works on 8bit images (convert if needed).