Flicker Program Status

The new version of Flicker which now runs as a stand-alone Java application is beta-level code. The following are known bugs, suggested features, functions that are being debugged or being developed, and resolved bugs.

Known BugsKnown bugs

  • 03-20-2004: There is no Flicker.lax file for the MacOS-X, Linux and Solaris systems. So the (Edit | Resize Flicker memory limits) command does not work on these systems at this time - it does on Windows.

  • 02-23-2004: The NTSC (R,G,B) image to grayscale option needs to be debugged. This will allow users to do quantification on the color image after it has been converted to grayscale. Otherwise, it uses the blue channel which of course biases the results.

  • 02-23-2004: Problem with Flicker not finding an image when you restart it with a previously saved .flk file if you have moved the image files to a different directory. This is because the .flk file saves the path and by moving the files, you have changed the path. Flicker has no way of knowing that you changed the path. You can either specify the files again, or edit the .flk file.

  • 02-23-2004: Problem where the Help menu entries that are supposed to pop up a Web browser - don't. This is because the browser is not configured correctly with the users operating system. The solution is to just go to the Flicker Web site through a separately launched browser. All of the links in Help are available through the Web site.

  • 12-17-2003: Allow gang-control of brightness/contrast range for both left and right images. This is useful if they were taken under the same conditions and have about the same initial contrast/brightness [Suggested by S. Lockett].

  • 12-17-2003: Need to zoom the positions of landmarks, and measured spots and circular mask in the new image scroller.

  • 11-10-2003: the (Transform | Poly Warp) menu command is not available. It needs to be debugged.

  • 11-09-2003: The (Transform | Pseudo3D) command does not remap the landmarks correctly after doing the pseudo 3D transform.


    Suggested FeaturesSuggested features / FAQ

  • 03-16-2004: Note on screen size. Flicker will work with a 1024x768 size screen. However, we find it MUCH easier to use with a larger screen (e.g. 1280x1024 works nicely). Because we are using AWT, it is difficult to optimize wasted whitespace in the main window. Until this is resolved, we suggest trying to run Flicker on a computer with higher resolution.

  • 03-16-2004: Gang scrolling only works if you use the Control-click method for scrolling the images. It does not currently work if you use the scrollbars. Normally, you would align the two images to the same spot using flickering, then enable gang scrolling. Then use the Control-click to scroll both images together.

  • 12-17-2003: Extend the brightness/contrast range [Suggested by S. Lockett].

  • 12-17-2003: Add option so that when do a (File | Open user images) command that presents images from a user directory, you can either generate pairs of serially comparable images (e.g., an ordered set of images from an optical or E.M. serial sectioning) or all pairs of images (the current default) [Suggested by S. Lockett].

  • 12-17-2003: Sometimes it does not restore the spot list that you have saved with a (File | SaveAs state file) and restored with a (File | Open state file) command.

  • 12-10-2003: The way we are implementing the image scroller does not allow you to center spots you select (Control-Press) with the mouse that are close to the edge of the image. the image. Currently these spots will not be centered since there is no image beyond the edge. We will be resolving this by adding a white space guard region around the edge of the image.

  • 12-09-2003: (GT) Images in all three canvases are getting cropped off at the bottom and right sides. When one compares the original image with the one displayed in Flicker (scroll to the bottom right) part of the image is missing. Changing the pagestep parameter in ImageScroller.java to 1 from 15 seems to help but there is still 5 pixels width missing. (JC) Related to this is that if you shrink the canvas size, it seems to readly cut off what is scrollable.

  • 10-31-2003: The (File | Open image file) and (File | Open image URL) menu commands are not available for color TIFF images at this time. It does work with grayscale TIFF images. Note that images with more than 8-bits of grayscale are scaled down to 8-bits losing the least significant bits.

  • 11-10-2003: Fix blackIsZeroFlag EVERYWHERE... need to have XxxxLoaders set it.

  • 11-10-2003: If do full quantification of 16-bit TIFF images, rethink keeping or re-reading 16-bit TIFF image data as (char iPix[]) if we are going to do quantification on that type of image without losing grayscale resolution.

  • 11-10-2003: Check and debug ImageXform.remapLMS() for Pseudo3D and PolyWarp transforms.

  • 11-10-2003: Check data structures, implementation, and debug the boundary drawing code for (Quantify | Measure by boundary) methods.

  • 11-10-2003: Check and debug measurements made on the Zoom image for magnifications different than 1X. It currently performs the measurements as if it were 1X.

  • 11-10-2003: Add vertical and horizontal 1D gaussian-like line filters for use with other types of data. E.g, here is an example of a filter to look for horizontal lines:
           0 0 0 0 0 0 0 0 0 0 0 0
           1 1 1 1 1 1 1 1 1 1 1 1 
           2 2 2 2 2 2 2 2 2 2 2 2 
           1 1 1 1 1 1 1 1 1 1 1 1
           0 0 0 0 0 0 0 0 0 0 0 0 

  • 11-10-2003: Get some better edge enhancement filters.

  • 11-10-2003: Add interactive rubber-band ROI window definition GUI.

    Resolved BugsResolved bugs

  • V0.83.4 07-21-2004: If you saved the Flicker state in a .flk file having zoomed one or both images, it does now rezooms the image(s) when you restart Flicker on that startup file.

  • V.0.78 03-16-2004: When using a zoom factor different from 1.0X, measured spots positions are not generated using (C-B) and (C-M) commands. However, if the spots were generated at 1.0X, they do zoom correctly.

  • V.0.68 02-23-2004: The paradigm was changed in the (File | Open user images | ...) so that it handles both "pairs of images" and "single images". This makes make it easier for a user to load say a standard active map gel (i.e. Swiss-2DPAGE map) in the left image, and then individual user gels into the right image for comparison.

  • V.0.68 11-10-2003: Added PopupODcalib() to popup a spreadsheet of values of (Step, OD value, Gray Value) editing window. This includes a histogram and OD vs gray Peak table of the step wedge pixels values inside of the Step Wedge ROI. You can mouse over and capture the peaks to edit the values.

  • V.0.68 11-10-2003: Saved an image calibration in a separate .cal file. This avoids having to recompute the calibration if we change the images. When you load an image, it can check for the corresponding .cal file and then load it and indicate that it exists.

  • V.0.66 2-14-2004: Modify spot circle overlays options so that it is easier to edit spots close together. Options being investigated include: a) showing only the last current spot; b) showing "+" for all spots except for the current spot; c) other options. [Suggested by Enrico De Toni]

  • V.0.61 01-31-2004: Fixed problem that if you started Flicker from a previously saved .flk state file by double clicking on it's icon, it did not completely restore the state. However, if you restored the state using (File menu | Open state file) it did it correctly. This fixed the problem that measured spot lists were not restored with the former, but were with the latter [reported by Enrico De Toni].

  • V.0.60 12-09-2003: (JC) Fixed a problem that the image is cropped when scrolling is that if you shrink the canvas size, it seems to cut off what should be scrollable on the right and bottom edges.

  • V.0.60 01-26-2004: Fixed bug that if you saved a Flicker state in a .flk file that pointed to some images that you subsequently moved or deleted on your disk, Flicker would hang and you would need to kill the process (e.g., Task manager in Windows). This has been fixed by reporting the problem and then exiting flicker. It is up to the user to either restore the image to the previous location, or to not use the .flk file. [Reported by Enrico De Toni].

  • V.0.56, 01-07-2004: Fixed bug in the image pipeline processing where if you zoom first and then do an image transform, it did not zoom the transform.

  • V.0.55, 12-27-2003: Fixed bug in the image pipeline where if you zoom first and then use the brightness/contrast filter, it did not use the zoomed image. Now you can use both zoom and brightness contrast and any other transform and it will do a (iImg > oImg > zImg > bgImg) pipeline processing. Of course, doing both zoom and brightness/contrast filtering will take longer. Doing a Reset images will clear the zoom and BC filtering.

  • V.0.54, 12-22-2003: Fixed the recent images database that updates DB/FlkRecentDB.txt save and restore state. It limits the history to the last 10 images. The (File | Open recent images) lists the images. It records single images from the (File | Open file image), (File | Open URL image). It also records pairs of images from (File | Open URL user images) and when you load a pair of images using the (File | State | Open state file).

  • V.0.53 12-18-2003: Fixed problem where it would jitter if you tried to flicker the images after doing a (File | Reset images).

  • V.0.49 12-12-2003: Fixed bug so can now save and restore correctly circular-mask measured spot lists you generated a series of circular mask spot measurements and saved with the (File | Save(As) state file) command.

  • V.0.43, 11-29-2003: Implemented fractional zoom using image sampling (no bin-linear averaging at this time) and changed the scrollbar so the center is 1X, left is fractional to 1/10X and the right is magnification to 10X.

  • V.0.41, 11-24-2003: Fixed bug introduced in version 0.37 when clicked on canvas, it failed under some conditions. Fixed the SaveAs state so that it saves more of the state and also restore the landmarks and position properly. When using the ZeroG installer, you need to enable Java applets and Java in order to use the default installer. The other other is to download the installer and save the file. Then run it on your computer.

  • V.0.41, 11-24-2003: Added log(grayscale) option to use when reading grayscale images more than 8-bits (e.g., 10-bit, 12-bit or 16-bit tiff grayscale images). This maps it in the TiffLoader.

  • V.0.37, 11-17-2003: Added Resize canvas menu and code to resize the three windows up or down using either menu commands or the "-"/"+" canvas resize buttons.

  • V.0.36, 11-14-2003: Fixed suble error in ROI rectangle drawing routine. Added code to let you define the ROI as between the C-U and C-L marks and it will flip their definitions if required.

  • V.0.35, 11-13-2003: Fixed ROI rectangle drawing routine in ImageScroller where the ROI rectangle is now drawn correctly if move the image scroller in and out of where the rectangle should be. Also fixed bug in copying the ROI to the computing window.
  • V.0.33, 11-11-2003: Implemented the (File | Update demo images DB) command that downloads the latest demo images and DB/FlkDemoDB.txt.

  • V.0.32, 11-11-2003: fixed bug where the (Quantify | Measure by circle | ...) and (Quantify | Background by circle | ...) menu commands generated negative background corrected data. Fixed use of blackIsZero.

  • V.0.31, 11-09-2003: the (Transform | Affine Warp) menu command was fixed. It also correctly remaps the displayed landmarks in the output image (oImg) where the transform resides.

    Contact us     Flicker is a contributed program available at open2dprot.sourceforge.net/Flicker          Revised: 05/15/2006