Flowtrace for Python
Implementation of the flowtrace tool as a module for Python 2 / Python 3
William Gilpin, Vivek N. Prakash, and Manu Prakash.
$ curl -OS https://github.com/williamgilpin/flowtrace_python/archive/master.zip
Or, using git
$ git clone https://github.com/williamgilpin/flowtrace_python.git
Somewhere in your script, include the import statement
$ from flowtrace import flowtrace
Run using all defaults and a 30 frame projection window
Subtract the median of every 30 frames to remove slow-moving background objects
Color the output streamlines to denote the direction of time
Adjust the number of cores that the code uses to multithread
API and Options
imagedir : str
- path to directory containing raw image files
frames_to_merge : int
- The numbe of frames to merge to form a single streamline image
out_dir : str
- path to directory where streamline files are saved
max_cores : int
- With multi-threading enabled, the maximum number of simultaneous jobs to run.
- When running this, it’s useful to calculate the total RAM available versus that required to completely hold an image stack of length frames_to_merge, since parallelization is not useful if there’s not enough RAM for each core to complete a task
frames_to_skip : int
- The number of images to skip when building each substack
invert_color : bool
- Set to “True” for dark objects moving against a white background
take_diff : bool
- Whether to take the difference of consecutive frames
diff_order : int
- The order of the difference in frames when take_diff is used
subtract_median : bool
- For each substack, subtract the median before taking the z projection
subtract_first : bool
- For each substack, subtract the first frame before taking the z projection
add_first_frame : bool
- Add the unaltered first frame of the stack back to the stack before taking z projection. Makes it possible to view sharp structures in median transformed data
color_series : bool
- Color the time traces
The code just won’t run
If you are consistently getting errors on your system, try disabling parallization with the setting
use_parallel=False. Multithreading in Python can be configuration-specific, and so flowtrace will not succeed in multithreading if Python’s multiprocessing library is not working.
$ flowtrace(‘sample_data’,30,’sample_output/’, use_parallel=False)
Certain combinations of keyword arguments might cause errors–for example, using median subtraction and inverting the color simultaneously might yield unpredictable results on color images.
The code is performing surprisingly slowly.
- If the code seems to be reading very slowly, try using Fiji or ImageJ to open the image sequence as a stack, convert to 8-bit tif (or RGB if using color) and then re-save all the files Even if the raw data is supposedly .tif, sometimes the encoding is funny and so scipy struggles to read the files.
Attempts to read or write files fail to find the appropriate directory (Windows only)
- Make sure you are using the correct format for filepaths on Windows. Instead of
Bug reports and pull requests are encouraged through GitHub