Useful ImageJ plugins (not written by me !)
I'm an active user of the ImageJ program. Here is a selection of ImageJ plugins I use constantly.
LOCI Bio-Formats : this must be the most useful ImageJ plugin. It allows to import and convert all the proprietary image formats that are used by many microscope and software makers.
Running Z Projector : by Nico Stuurman. This allows to average images in a stack using a running average. Can be used to enhance S/N in a time-lapse serie (at the expense of the temporal precision), or to compare static and moving objects by substracting averaged stacks to the original data.
Align RGB Planes : by Gabriel Landini. Using this plugin you can register different channels by shifting them manually. Usefull if you have a shift between two channels due to misaligned filter cubes or to drift during stack acquisition on a confocal microscope.
Image Stabilizer : By Kang Li. Automatic stabilization by registration using the Lucas-Kanade algorithm. Very efficient to correct stage drifts in long time-lapse series, if your sample doesn't move too fast !
NeuronJ : by Erik Meijering. This plugin can semi-manually trace fluorescent neurites, like a "magic wand". It allows to quantify fluorescence intensities along axons and dendrites of cultured neurons images very rapidly and reproductibly. For a 3D version check Simple Neurite Tracer that is included in Fiji, a supercharged version of ImageJ.
MTrackJ : by Erik Meijering. A semi-manual tracking plugin that can snap to the local intensity maximum and allow to rapidly track objects. Also contains a lot of rendering options to display tracks.
my ImageJ macros
The ImageJ macro language is well suited to automate repetitive tasks and processing workflows. To use one of these macro, just save it as text files from your browser, drop it in your ImageJ plugin folder, and they will appear along your other plugins in the Plugins menu after ImageJ restart.
Batch conversion macros
These macros allow to extract images from proprietary formats such as Leica .lei/.lif, Zeiss .zvi or Metamorph .stk files. You'll need to install the LOCI Bio-Formats plugin that can be downloaded here by dropping the loci_tools.jar in your ImageJ plugin folder.
LIF Extractor : this macro extracts .lei and .lif multichannel Z-stacks into multiple .tif stacks, splitting the channels into different stacks. Several options are possible such as background substraction, various filters, or optional reset of spatial scale.
LIF Projector : this macro is similar to the LIF_Extractor, but it will output Z-projection of each Z-stack. You can choose the type of projection in addition to the other options.
ZVI Extractor : this macro allows to batch convert .zvi multichannel time-lapse movies into .tif stacks. There are several options for processing and filtering. In particular, you can register the jitter due to small stage movements during acquisition. For this option to work you need to install Kang Li's Image Stabilizer plugin.
STK Extractor NoLabel : this macro allows to batch convert multichannel .stk file made by the "Acquire Multiple Wavelength" mode in Metamorph. It will just convert them to a series of single tif images with a number appended for each channel.
Stack Processor : this macro can batch process image stacks in a folder with various enhancing and filtering options.
Process&Overlay : this macro starts from a folder containing series of images representing multichannels acquisitions and allow to batch enhance them before processing overlays.
Transfer Labels : Sometimes a processing step will loose slice labels in a stack, which can be very bad for identifying images. This macro allows to copy slice labels from one stack to another, with the option of replacing a part of the slice label from the source stack by a defined string in the destination stack (for example, you can transfer labels that all ends with "_ch01" in the source stack, to a destination stack, changing the end of all labels to "_overlay").
Shuffler : This macro copies all images from one folder to another, randomizing names but keeping channels from the same image grouped. This is useful for blind quantification of images.
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