Analysis of movement

cellprofiler

#1

Dear Team,
I am trying to use cellprofiler for analysis of movement. My objects are very small ranging from 2,12 pixel and there are lots of objects (approx 2000) in each frame . Tracking objects is difficult as I have already communicated. I am trying to study movement using morph - Skel module. Is it possible to measure total movement or changes frame to frame (in a movie)? If yes, how we can do that?
I am using Load module-Rescale intensity-Identify primary automatic-Morph(Skel)-Save images(avi-8bit-Movie).
Best,
A


#2

In fact I am unable to use save image module even whatever format I choose and whatever bit depth I try to choose.
This is the error being thrown out-

There was a problem running the analysis module SaveImages which is number 06. Error using ==> iptcheckinput
Function STRETCHLIM expected its first input, I or RGB,
to be one of these types:

uint8, uint16, double, int16, single

Instead its type was logical.

Stack:
ParseInputs in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\toolbox\images\images\stretchlim.m (85)
stretchlim in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\toolbox\images\images\stretchlim.m (42)
SaveImages in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\Modules\SaveImages.m (361)
AnalyzeImagesButton_Callback in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10442)
gui_mainfcn in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12182)
CellProfiler in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)

Can you let me know where I am doing wrong settings.
Anil


#3

Hi Anil,

[quote=“htscdri”]In fact I am unable to use save image module even whatever format I choose and whatever bit depth I try to choose.
This is the error being thrown out-

There was a problem running the analysis module SaveImages which is number 06. Error using ==> iptcheckinput
Function STRETCHLIM expected its first input, I or RGB,
to be one of these types:

uint8, uint16, double, int16, single

Instead its type was logical.[/quote]

To correct this, specify “No” for “Do you want to rescale the images…” in SaveImages.
-Mark


#4

Thanks Mark for your reply,
Can I load two consecutive images from same source with load image module by regular text expression for a movie analysis? I do not wish to duplicate data cutting one frame from each of dataset and putting in two different folders which I think would be possible but at the same time it consumes data storage space. Precisely I would like to see movement changes between two frames in a movie, can I tell load image module to take from frame 0-19 as first image set and from frame 1-20 as second image set through text regular expression?
Thanks in advance
Anil


#5

Hi Anil,

Unfortunately, CellProfiler doesn’t offer functionality to select individual frames from a movie, although using the GroupMovieFrames modules, you can split up the frames in a variety of ways. If you do wish to save a truncated version of an avi movie, you can use the SplitOrSliceFrames module to do so.

Regards,
-Mark