Computer Science » CellTracker User Forum

Re: Installation

A guest user — Fri, 13 May 2016 14:39:15 GMT

Did anyone manage in the recent months to install the software? I am having similar issues to the ones mentioned here without seeing any resolution.

Re: Installation

A guest user — Sat, 03 Oct 2015 22:36:35 GMT

In this post Chengjin Du wrote:

Could you please go to the website of https://files.warwick.ac.uk/cdu/browse#sendto to download the MCRInstaller.exe file and install it into your computer, that should solve the problem.

I colud not solve the problem although I installed the MCRInstaller.exe file.

Re: Installation

A guest user — Thu, 23 Jul 2015 16:33:32 GMT

Downloaded file and other things too , but nothing works.

What's going on? Is the software still available maybe as an up to date version?

Re: Installation

A guest user — Mon, 15 Jun 2015 22:28:54 GMT

I have successfully installed the software and required programs.

But when i tried to open it, a black colored screen of celltracker appeared shortly and disappered.

What is the issue here? I am using on window 7.

Thanks.

Re: Installation

A guest user — Mon, 15 Jun 2015 22:15:36 GMT

Hi, in the installation instructiion sheet, I notice that "Currently, we only supply the software compiled via Matlab R2008a". I am using Matlab R2013a. So, does it mean that I cannot use CellTracker. Or anything I can do to use it? Thanks

Re: User Interface

Paul Brown — Thu, 08 May 2014 09:56:31 GMT

Have now completed the boundary editing functions. Boundaries can be resized and rotated

Edits can now be synchronised betweewnselected frames via the gallery form

Shortcut keys now allow boundaries to be copied and pasted

Re: User Interface

Paul Brown — Wed, 05 Feb 2014 15:44:43 GMT

Labelling now completed. Lables are added via the object's context menu. They are edited and deleted via their own context menu. THere is now no global 'labelling' mode. Lables can be added, edited and deleted at any time. They can also be dragged around with the mouse independently of the object they belong to, with a line joining them to the object.

Clicking on a frame in the gallery now takes the main form to that frame

Re: User Interface

Paul Brown — Wed, 05 Feb 2014 15:42:03 GMT

The following requests were made

Boundary edits to be synchronised across selected frames
Boundary copy and paste keyboard shortcuts
Add/delete spline points function
The ability to delete boundaries via the gallery view
Export individual pixel values so tiff images can be created
Excel does not correctyl align data from a cell that appears in the middle of tracking. It is added to top of spreadsheet when it should come at correct timepoint further down
THe ability to concatenate lsm files that are the same location but different times
The ability to choose exactly which cells to export to Excel
Fix keyframe tracking and restrain the variation in size of nucleus between frames to prevent unrealistic changes
Advanced cell tracking motion paramters don't work

Re: Installation

A guest user — Mon, 27 Jan 2014 12:58:42 GMT

Could you please go to the website of https://files.warwick.ac.uk/cdu/browse#sendto to download the MCRInstaller.exe file and install it into your computer, that should solve the problem.

Re: Installation

A guest user — Sun, 26 Jan 2014 09:14:55 GMT

Hi, after installing the software, I was notified that 'the program can't start because mclmcrrt78.dll is missing from your computer. Try reinstalling the program to fix this problem.'

I have tried to reinstall the program but the problem is not fixed.

May I know what can I do to resolve this problem?

Re: User Interface

Paul Brown — Thu, 16 Jan 2014 23:05:46 GMT

Edits are now saved immediately, rather than only when changing frame or switching off editing.

Boundary/ROI labelling has been modified and improved. Labels are now added via a context menu. Their positions and text are saved whenever they are deleted as a result of a frame or channel change. They should always be up to date when redrawn. They are moved with the BD/ROI when in edit mode. These can now be moved with the cursor keys.

A number of problems with multi-channel views have been fixed. It is now possible to add and edit boundaries and regions of interest in this view and changes are synchronised between the views.

Bug fixes to stop cases were editing turned off when lines redrawn

Re: User Interface

Paul Brown — Tue, 10 Dec 2013 15:40:04 GMT

The gallery view is now complete. It is now updated in real time in response to the user applying pre-processing and adding or editing boundaries or regions of interest.

It is now possible to add and edit boundaries and regions of interest when viewing more than one channel. Any channel can be edited and they are synchronised.

Re: User Interface

Paul Brown — Thu, 28 Nov 2013 10:25:13 GMT

The gallery view is now almost complete. The gallery form is launched from the main form and displays thumbnails of every nth image. Channel can be selected independently of the main form. The gallery view is synchronised with the main view whenever on of the following events occurrs

A ROI is added
A boundary is added, edited or copied
Pre-processing parameters are applied

So far I am not sure if the correct updates are applied after tracking has taken place. This is what I am working on at present.

Re: User Interface

Paul Brown — Mon, 28 Oct 2013 12:35:30 GMT

Here are a list of priorities for the interface. These features seem to be the most widely requested and the most useful

The ability to save boundary changes without changing frame.

A gallery view that allows the following

parameter changes to be previewed across the entire time series
boundary edits to be applied to multiple frames
the accuracy of tracking to be assessed across the entire time series

The ability to save different parameter sets for different types of experiment.

Re: User Interface

Paul Brown — Mon, 28 Oct 2013 12:10:12 GMT

In response to user feedback, I have added the following new suggestions for the user interface

Boundary Selection

The ability to use the copy and paste keyboard shortcuts would be useful when working with boundaries

A function to globally select all boundaries

A button to 'add new cell'

Tracking

The ability to tell cell tracker to 'stop tracking this cell', should a cell divide during the experiment.

Fix the issue whereby if a tracked cell goes out of frame, this is not flagged up but prevents export to Excel at the end.

Parameters

The ability to specify a maximum fluorescence intensity value, as well as a minimum. This would allow very bright dead cells that can appear in frame to be ignored.

The '% pixel movement allowed' parameter is hard to relate to the image. Draw the range of movement this represents

Exporting Data

Export other quantifiable properties, such as size of the cell tracked.

The ability to export to a worksheet of an exisiting workbook as well as creating a new workbook. This would make it easier to group experiments together and keep track of them all.

A means of linking a cell tracker session file to corresponding Excel workbook.

Export data in other formats, such as XML.

Miscellaneous

A prompt is required when exiting asking for confirmation. It is too easy to select the Exit menu item by mistake.

User Interface

Paul Brown — Thu, 26 Sep 2013 13:11:52 GMT

Here is a list of feature requests and bugs that relate to the user interface

Boundary Selection

Tracker can’t cope with > 200 regions of interest.

Show/hide boundary function e.g on right mouse click would be useful to check whether boundary was in correct position without having to move it away then attempt to replace it.

A nudge function with cursors like when moving objects in powerpoint would be good too.

Want to be able to grossly resize areas of interest about centre without moving all the edit points, also rotate about centre

Mouse icon doesn't show whether moving edit point or entire shape

Turn off automatic pickup of whichever edit point the mouse crosses, just stay with the one you started with.

Resets boundaries after editing back to the beginning during another task e.g. drawing new boundary or adding label unless you advance frame and go back again first, therefore impossible to edit last frame

When zoomed in can't scroll round image. You have to zoom out then back in further along and reselect edit points function.

Add and delete points on boundary would speed up boundary editing.

You can’t delete or add end points on spline curve.

Programme needs reminding which function it is using after deleting boundary

You can't delete all boundaries at once - Tracker seems to be unable to see some boundaries

Deleting boundaries box should not automatically highlight any boundaries as this makes it easy to delete by mistake

Boundary labels would be useful when analysing multiple cells in one field but would be helpful if labels could be moved say from one side of boundary to the other to avoid obscuring regions of detail.

When boundary is labelled, the labels don't move with boundary

No way to recover cell boundary groupings if get out of synch, have to start again

Allow cursors to control moving to next/previous frame

Simultaneous editing of boundaries in consecutive frames using gallery view

When a boundary is adjusted, there should be an option to remember this for subsequent frames so one doesn’t have to keep changing it for all frames.

Have to move to next frame to accept changes to boundaries

Error positive integer - boundary out of frame prevents export. Why can't it say which frame contains the error rather than leaving it to you to go through every single one again

Tracking

Tracking automatically adds boundaries to all frames if first frame had them on

Need more options for model-based tracking of the nucleus. Not always an ellipse.

To input range for tracking, programme should highlight current frame as start of range automatically.

Gallery view of thumbnail images would be useful for a quick overview of how well tracking had gone without loading each image separately. Would then be able to process boundaries to ellipse where necessary simultaneously (command exists within processing window but is unusable at the moment except for individual frames or short runs)

Parameters

Gallery view would also be helpful when setting pre-processing parameters so you can check easily that pre-processing is suitable for more than just the first frame e.g. if could look at every 10th frame.

Tool to measure intensity anywhere you like on the image e.g. if mouse over a point would be useful to set thresholds to reasonable values without too much trial and error.

Cytoplasm parameters detection limit preview in simple cell tracking bears no resemblance to result from cell tracking

When using cell tracking, programme requires user to open parameters boxes and click ok even if wanting to keep all parameters on default settings.

Be able to save sets of parameters for tracking eg if tracking nuclei separately from cytoplasm, rather than return to default each time. Need a list of experimental protocols and corresponding parameter sets.

Need suggested range for all parameters and whether linear/logarithmic.

Exporting Data

When exporting data to Excel, currently Tracker puts all cells from one field (one analysis session) on one sheet. Exporting each cell to a new sheet would improve automating the later part of data analysis, including graph production.

Ability to get raw numerical data from cell profile would be useful, rather than just the graph.

When saving files, offer the folder the time series came from automatically.

If all boundaries are cellular and called cell 1, 2, 3 etc, a problem arises when the number 10 is reached. When exported to excel, it places in the order 1, 10, 2, 3, 4 etc. i.e. using name as all text rather than text and number value

export profile (bisect) data as numbers not graphs?

Miscellaneous Bugs

The function cellwatershedpreview, called by the Cell->Simple Cell Tracking->Cytoplasms->Parameters->Preview menu may crash when the image is stored as uint16 rather than uint8

When using the Cell->Simple Cell Tracking->Nuclei->Nuclear Shape, Size an Location don’t’ change option or the Cell->Simple Cell Tracking->Cytoplasms->Little or Limited change in shape and size option, there is an undefined function ‘Ncpt’ error message.

When manually measuring borders and attempting to find ‘Default cell motion parameters’, by specifying ‘Frame range for estimating motion parameters’, there was an undefined function ‘arfit’ message.

When exporting to Excel there was a ‘usbscript indices must be real positive integers or logicals’ error at bd_props2->overlay2cell at line 297.

If using save and close, then cancel save operation say because of wrong file name, program closes without saving at all.

User Meeting 25th October 2013, Manchester

Till Bretschneider — Fri, 20 Sep 2013 11:46:56 GMT

The user meeting will be held in Manchester, Room B.4208 in the Michael Smith Building, on Friday 25th October, 2013, from 12:30 – 5pm.

Please click this link to register.

Experiments

Till Bretschneider — Fri, 20 Sep 2013 11:04:49 GMT

Please give a rough description of what you are using CellTracker for

Wish List

Till Bretschneider — Fri, 20 Sep 2013 10:02:04 GMT

Please comment on any functionality you would like to see implemented

Algorithms

Till Bretschneider — Fri, 20 Sep 2013 10:00:50 GMT

Segmentation related issues

1. Tracker appears to have been trained on reasonably round cells e.g. HeLa. Would be useful to be able to alter boundary parameters to allow better tracking of more convoluted edges with lots of protrusions for some cell types compared to the more rounded ones. Suggested ranges and explanations for any parameters needed to manage this would be helpful.

The active contour method segment the image via minimising an energy function which is related to the curvature of the boundary. The round cells will have lower energy and is preferred by the algorithm. On the other hand, the method also incorporates the intensity information into the energy function. In other word, it depends on the contrast of cells with more convoluted edges and lots of protrusions. If the contrast is high enough, it should be segmented properly. The problem is that for most of the cell types the contrast is low, which leading to the segmentation in round shape. In theory, we can decrease the weight of curvature related energy term to allow edges to be more convoluted, however, other issues such as boundary might cross itself might arise.

2. Boundary shouldn't be allowed to cross from dark to light to dark again or vice-versa

It is difficult to define what is "dark" and "light", since the intensities of nucleus and cytoplasm change dynamically. In some cases (e. g. the protrusion region), it is actually allowed to cross from dark to light to dark again.

3. Recognise contours rather than just threshold, might be helped by using edge detection tool

The output boundary is based on the segmentation results, not just threshold the image. Segmentation by using edge detection tool is only suitable when the image intensity are quite homogeneous. For cell images, many edges will be detected due to the noise, which is hard to choose the right ones and connect them together to form a closed boundary.

4. Penalty for deviating from ellipse/diamond shape might help draw cytosol boundaries sensibly in low-intensity frames.

You are certainly right, it will help draw cytoplasm boundaries sensibly in low-intensity frames by adding a penalty term for deviating from ellipse/diamond shape. A segmentation method with ellipse shape prior should be developed.

5. Force boundaries between two cells not to cross a user-drawn line

The user-drawn line can be consider as hard constraints provided by the user. By enforcing such kind of hard constraint into the energy function, the two cells will not allowed to cross the user-drawn line.

Tracking related issues

1. Boundaries must stay within frame even if cell moves out of view.

This is a problem on how to deal with the situation when the tracking is lost. We can put a fake boundary within the frame by assuming there is no motion, which will give wrong information in most of the cases. Sometimes, it is quite difficult to tell whether the tracking is lost or not due to the similar appearance of different cells or the changing of appearance.

2. Might be helped by using track as ellipse then refine edges function, but can't get snake parameters on refine active contours to do anything useful

The current method use the boundary in the previous frame as the initialization of the active contour and then refine the contour, which is more reasonable for most of the cases. When the segmentation going wrong, it will be better to use ellipse and then refine it. The question is where we should put the ellipse when the tracking is wrong. As in most cases, the wrong tracking is caused by the low intensity of cell, and it will not work well by just changing the parameters to refine the contour.

3. If using key templates tracking function would be useful to be able to detect cells in all key frames in one go using same parameters rather than each individually

We can do this by combine the key frames into a 3D stack and segment it in one go, however the accuracy will not be guaranteed, especially when the cell changes dramatically in time.

4. Use threshold between values rather than simply above threshold for tracking cytoplasm

The tracking of cytoplasm is not based on refining the active contour initialized by previous frame, not on the threshold.

Topology related issues

1. Nucleus boundary must stay within cytoplasm boundary.

In the current implementation, the nucleus and cytoplasm are segmented separately. To tackle this problem, we are going to develop a method which preserves the topology of nucleus and cytoplasm by integrating knowledge about topological properties.

2. Nucleus boundary must not overlap cytosol boundary, one boundary must not overlap another

Introducing the inter-repelling mechanism and enforcing the topology constraints should solve the problem.

3. Boundary shouldn't be able to cross itself

Again, this is a topology problem, currently not implemented.

Cell type related issues

1. Can you save a set of parameters for each cell type rather than having to alter them all by hand if you move from one cell type to another?

We can tune the set of parameters to optimise the performance according to the specific type of cells, and save them into a configuration file. Every time before running the algorithm, you need to load the configuration file first. We need at least 3 data sets for each type of cell to tune the parameter. If you think your data is different from others, please upload 3 data sets to our server.

2. Need suggested range for all parameters and whether linear/logarithmic, need suggested values for each cell type to improve tracking

The parameters are depending on the image data. We will test the different type of cell images and provide a suggested range for all parameters, and a configuration file for each type of cell.

3. Maintain set parameters rather than return to default each time, would be even better to be able to save sets of parameters for tracking e.g. if tracking nuclei separately from cytoplasms

See above.