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CellTracker User Forum

CellTracker User Forum User Interface

  1. 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.
  2. User Meeting 25th October 2013
    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.
  3. User Meeting 25th October 2013 - Priorities
    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.
  4. Progress update
    The gallery view is now almost complete. The gallery form is launched from the main form and displays thumbnails of every/n/th 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.
  5. Progress update
    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.
  6. Progress update
    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
  7. Manchester Meeting 17th Jan 2014
    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
  8. Progress update
    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
  9. Progress update
    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