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I have tiff image stacks of 1000 frames in which I'm trying to track particles diffusing in Brownian motion. So I'm using trackpy for particle tracking: import the tiff stack, locate the features (particles) and then plot their trajectories. I'm using the following code (as from the trackpy walkthrough page):

import pims
import trackpy as tp 
frames = pims.open("image.tif")
f = tp.locate(frames[0], 9, invert=False)

But this last line (tp.locate) gives a traceback:

AttributeError                            Traceback (most recent call last)
<ipython-input-78-0fbce96715a7> in <module>
----> 1 f = tp.locate(frames[0], 9, invert=False)

~\anaconda3\lib\site-packages\slicerator\__init__.py in __getitem__(self, i)
    186                 indices, new_length = key_to_indices(i, len(self))
    187                 if new_length is None:
--> 188                     return self._get(indices)
    189                 else:
    190                     return cls(self, indices, new_length, propagate_attrs)

~\anaconda3\lib\site-packages\pims\base_frames.py in __getitem__(self, key)
     96         """__getitem__ is handled by Slicerator. In all pims readers, the data
     97         returning function is get_frame."""
---> 98         return self.get_frame(key)
     99 
    100     def __iter__(self):

~\anaconda3\lib\site-packages\pims\tiff_stack.py in get_frame(self, j)
    119         t = self._tiff[j]
    120         data = t.asarray()
--> 121         return Frame(data, frame_no=j, metadata=self._read_metadata(t))
    122 
    123     def _read_metadata(self, tiff):

~\anaconda3\lib\site-packages\pims\tiff_stack.py in _read_metadata(self, tiff)
    124         """Read metadata for current frame and return as dict"""
    125         # tags are only stored as a TiffTags object on the parent TiffPage now
--> 126         tags = tiff.keyframe.tags
    127         md = {}
    128         for name in ('ImageDescription', 'image_description'):

~\anaconda3\lib\site-packages\skimage\external\tifffile\tifffile.py in __getattr__(self, name)
   2752             setattr(self, name, value)
   2753             return value
-> 2754         raise AttributeError(name)
   2755 
   2756     def __str__(self):

AttributeError: keyframe

where I'm going wrong? I also tried using

imageio.imread("image.tif")

to import the image and then used

f=tp.locate(frames[0], 9, invert=False)

to locate the particles. But the output of this is supposed to be data for both x and y coordinates, like so

enter image description here

whereas what I get is just for the x axis:

enter image description here

James Z
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Arti Tyagi
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1 Answers1

1

I just had this same problem and solved it by entering "conda install pims" into my anaconda prompt. I had done "pip install pims" before, and I think that messed it up.

Ralph Brockman
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  • Thanks, what I was doing wrong here was to import the file as a tiff stack (like a video). It worked when I saved the stack as 1000 individual images in a folder and then imported the folder using pims.open("folder_path/*.tif) – Arti Tyagi Apr 14 '21 at 08:38