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Protocol List

Current number of protocols: 50

3
This protocol automatically quantifies the fluorescence in preimplantation mouse embryos. Tutorial to use ...
This protocol automatically quantifies the invasion rate of pathogens in a 3D tissue model. It calculates the ...

4
This protocol takes a folder with four channel images as an input and creates three separate three-channel ima...

a
2D or 3D automatic registration based on spot detection and on ECclem AutoFinder. Can serve as pattern search ...

b
Complete detection protocol with 3 outputs: excel, binary, and detection screenshot
This protocol show an example about how to process very big image plan by region using the new loop Sequence F...

c
This protocol will process a complete folder of image and automatically calculate the size of top object knowi...
Protocol used to analyse the datasets from the 2015 cell tracking challenge
This protocol counts the number of cells with signal aggregates in the neighborhood of cell nuclei (Golgi apar...
Protocol measuring the cellular internalisation rate of chlamydia based on two fluorescence reporters (one for...
Display detections performed in 2 channels and colocalized detection.
This version automatically name the xls and binary output files
This protocol computes the Pearson and Manders coefficients between 2 spotty images (the masks of spots that a...
This protocol extracts the statistical percentage and distance of colocalization between 2 color molecule spot...
This protocol duplicates the input sequence as well as the ROI that are selected by the user
This protocol crops the input sequence to the bounding box of each ROI (thus producing a list of cropped seque...

d
This simple protocol detect some spots inside a channel and cells in another channel then it use the ROI inclu...

e
This protocol will export statistics in excel format of all image available in a folder. If a ROI is present ...
Extract channels from a sequence to display or process them individually

f
This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and grows a co...

g
This protocol performs a smooth on the image.

i
This protocol show how to apply the ImageJ "subtract background" command image by image on a whole Z stack.
This protocol uses a "folder loop" block to read every tif file in the specified folder and run an automated t...

l
This protocol saves series of a lif file as single tif file into a new folder named as the lif file. Series ar...
Allow the conversion of LSM files from a folder into TIFF files. Files are saved in the same folder.

m
This protocol compute the maximum Z projection for a whole folder of image (support multi serie image). By de...
Perform a median filter on the active sequence using the ImageJ rank filter plugin, and convert the result bac...
This protocol will do a single 2 channels image acquisition using Micro Manager for Icy.
This protocol will do a 3D Z stack image acquisition (2 channels) using Micro Manager for Icy.

n
This protocol ask for a nd file and convert all acquired series in individual sequence files. There are saved ...

o
This protocol computes the optical flow of a 2D+T sequence. The results are displayed with flow arrows pain...

p
PACT is aimed at dealing with large fluorescence microscopy datasets. It performs a first rough segmentation o...
For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.
Simple example to show how to iterate over all frame of a time sequence and process then independently.
This protocol, designed for the microbiology course at Institut Pasteur, allows to extract cell masks, and act...

r
This protocol is a simple demonstration of some ROI tool blocks: - Separate ROI components - Filter ROI - D...

s
This short protocol is an example to save a sequence with a modified name at the same hierachical level than t...
This protocol takes a folder containing images as input and extract each channel in a separate sub folder.
Simple protocol to change the pixel size information of all images contained in a folder.
Detects spots and save it in an excel file, in the same folder as the source file.
This is the first protocol with spot detection for test purposes.
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol shows how to use the new Spot Tracking blocks inside a Protocol. It does the following tasks : ...
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol counts the number of stained cells in a population of cells. It requires at least 2 color channe...
This protocol detects stress granules within cells using fluorescence imaging and quantifies their aggregation...

t
Just for testing
Threshold with multiple ROIs.xml
Detects and tracks cells in a 2D or 3D time-lapse sequence using active contours, and produces a list of ROI w...