extra:faqs

Much of FAST has been designed to limit user interaction with the GUI when this could cause data processing issues. These design choices include:

  • The inability to open more than one module at once.
  • The inability to interact with a module's GUI while data processing is ongoing.
  • The inability to access later modules before earlier processing stages have been completed.

Nevertheless, you may have legitimate reasons to override these choices. For example, when generating kymographs, you may wish to simultaneously use the overlays module to find the indices of interesting looking cells. If you are using the Matlab-based version of FAST, you can disable many of these features by editing the 'homePanel.m' file and changing the line

debugSet = false;

to

debugSet = true;

Note that data and program stability is not guaranteed if this change is made. You apply it at your own peril!

Yes, but you will first need to stitch your tile into a single, contiguous set of pixels for each channel at each timepoint. There are many tools to perform this task available on the web, such as ImageJ's Image Stitching plugin.

These stitched tiles should then be compiled into a single multi-frame/multi-channel image, which is saved in the root directory.

Yes. To do this, first split your dataset into each separate field of view and save each as an image file in a unique folder. For more details on how to set up your directory structure, please refer to the data configuration page.

Image cytometry is a simple alternative to flow cytometry, where microscopy is used to assess the fluorescence and morphological properties of thousands of cells simultaneously. After the appropriate experimental preparations, a single 2D image of a field of cells is taken and processed to extract useful information. It can be used, for example, to quantify the size of populations of cells labelled with different fluorophores, or to quantify the effect of different experimental conditions on the expression of specific proteins.

To use FAST to analyse image cytometry data, simply save each image in its own folder as described in the data configuration page. When analysing single frames rather than time series, the feature extraction module will output single timepoint-long 'pseudotracks' which can be analysed much like normal tracks.

  • extra/faqs.txt
  • Last modified: 2020/07/01 12:31
  • by pseudomoaner