Automated

quickPALM

Workflow
Description
QuickPALM is a set of programs to aid in the acquisition and image analysis of data in “photoactivated localization microscopy” (PALM) and “stochastic optical reconstruction microscopy” (STORM). QuickPALM features the associated QuickPALM ImageJ plugin, which enables PALM/STORM 2D/3D/4D particle detection and image reconstruction in ImageJ.
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Moment thresholding (ImageJ)

Component
Description

This method allows to compute a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose Moments in the list. In Aphelion, the tool is in Segmentation->Threshold->AphImgMomentThreshold The original paper is 2449

has topic
Bioimage informatics
has function
Image segmentation
Image thresholding
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Image anonymisation

Workflow
Description
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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Track cell intensity

Workflow
Description

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

has function
Active contours
Cell tracking
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Extract_Images

Component
Description

A utility macro for the specified use of BioFormats plugin. Takes a folder of proprietary images formats (Zeiss zvi, lsm, czi or Nikon nd2) and extracts them to .tif images

The extracted images are located in a folder defined in the menu. Other options: reset spatial scales, reads ROIs, split channels, add stage position in the name.

<!-- [previous text] 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. -->

note: The old name of the macro was "ZVI Extractor" and the data format was limited to ZVI, but the upgraded version includes more formats.

Requires Bio-Formats plugin

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