Opening a stacked image

Hi there, i've been having problems opening a load of images ive got for a while now and i just can't seem to get photoshop to do it right. So ive come here for some advice/tips.
Basically i have some micrographs ive taken which consist of 4 stacked images, a brightfield image (Grayscale) followed by 3 images in the RGB channels, i mainly just want the RGB images however when i open them in photoshop (currently CS4) all I get is the gray channel and the first image, no other channels/layers/stacks are available, i've tried lots of different approaches but i can't seem to get them to work.
However I can open them in Fiji (Image J) and I can edit them how i'd like (remove the brightfield channel but keep the rgb channels and edit the levels) but i have a large volume of pictures to run through (several hundred) and the automation on fiji isn't working properly. I'd use the automation on photoshop which would work brilliantly if i could only get them to open.
I really dont wont to have to edit every single individual picture in image J which is my only real option at the moment so please any help would be greatly appreciated. Ive uploaded a sample image and a edited image here:
http://rapidshare.com/files/375080934/Sample_Images.zip.html
and also
http://www.megaupload.com/?d=HDT7AENE
Cheers for any help!

Well is there anyway or format I can convert them to without having to split up and remake all the stacks. In the end I want to play about with each channel seperately and I have several hundred to go through so splitting them up and i'd end up with close to 500 pictures to put back together.
Is there a format i can convert them to which seperates the stacks into channels? Or some software which can do it as a batch process? I'm currently using ImageJ which can do that but the batch processing doesn't seem to work (it keeps coming up with error messages, and theres not exactly much in the way of support sites for it). I'd prefer to keep them as tiffs or other file formats which can keep the intensity value data and other bits picked up by the microscope.
Cheers for any assistance

Similar Messages

  • Script to open a multi-image TIFF into a layer stack?

    I have a colleague who has multi-image TIFF files, each of which contains a series of images of microscopy sections. He needs Photoshop (Mac version) to read these files, and place the multiple images into a stack of layers in one document.  We have found indirect ways of doing this, but they require multiple applications and several steps.  Is it possible to create a Photoshop script that does this directly: opening the multi-image TIFF, parsing the file, and loading the images into layers?  Does such a script already exist?  If not, can you point us toward source code samples that will help us build the script: perhaps snippets for parsing a multi-image TIFF, and initializing a document with multiple layers.
    Thank you.

    Chris Cox wrote:
    I've been trying to find a good way to handle multi-image TIFF files without excessive slowdowns and problems -- and haven't found a good solution yet.
    The ability to open other than the first page of a multi-page tiff would be welcome. Even if each page is opened as a separate document. Something similar to the way PDF files are handled now.
    Once all the pages of the tiff file where open the user could then choose the colorMode, bitDepth, etc to use if they wanted to combine the pages into one doc as layers. And as Xbytor points out if smart object layers are used there would be no need to convert when combining.

  • Batch: Open Bridge 'Stacks' as layers in PS CS5 + run action. Is this possible with script??

    I posted this topic a couple of days ago - I didn't know about this forum/group so the thread appears in Photoshop Scripting and Bridge Windows. I haven't found a solution on those forums - can any one here help?
    http://forums.adobe.com/thread/880777?tstart=0
    http://forums.adobe.com/thread/880779?tstart=0
    I would like to automate part of my workflow that involves opening stacked images (in Bridge CS5) as layers in Ps CS5 and running an PS action that composites the layers and processes the image. Something similar to 'Process Collection' in Bridge CS5 only with my own action instead of merge to HDR/Panorama.
    Apparently this is possible with Mac 'Automator' - is there anything I can do in Windows? I don't have any experience with writing scripts, but have friends that can help. Can someone tell me if its possible and point me in the right direction please?
    This needs to be a batch process. I know how to open images as layers from Bridge so that I can manually run the PS action - I would like to automatically process lots of images in this same way.
    To clarify, the script if possible will need to
    1) find first stack (in Bridge [in selected folder])
    2) open as layers in PS
    3) run PS action
    4) save and close (as psd preserving layers)
    5) find next stack in Bridge (selected folder) and repeat.
    By 'stack' I mean a set of similar files (for instance same scene -2EV, 0EV, +2EV)
    Bridge's 'Process Collection' feature is great because it very cleverly recognises similar images (I think you have to stack them first) opens them and either processes them into a hdr or panoramic image. Instead or hdr or pano, wouldn't it be great if you could run your own action.
    Bridge's Image Processor is fantastic at opening a batch of individual files and running your own processing action, but it won't open groups of images ('Stacks' or sets) as layers.
    What I need is basically a hybrid of the two.

    In case you miss my late append in the other thread you may want to look at the auto collection script that ships with the Bridge and use it as a base for what you want to do. You may also be able to automat the creation of your stacks if their time stamps are close. The Auto Collection Script night now does two types of stacks  HDR and Panoramas.  You may be able to modify it to do a third stack type. You stack type and use your stack processing process instead of mearge to HDR or PhotoMerge.
    From Bridge help:
    The Auto Collection CS5 script in Adobe Bridge assembles sets of images into stacks for processing as high dynamic range (HDR) or panoramic composites in Photoshop CS5. The script collects images into stacks based on capture time, exposure settings, and image alignment. Timestamps must be within 18 seconds for the Auto Collection script to process the photos. If exposure settings vary across the photos and content overlaps by more than 80%, the script interprets the photos as an HDR set. If exposure is constant and content overlaps by less than 80%, the script interprets the photos as being part of a panorama.
    Note: You must have Adobe Bridge with Photoshop CS5 for Auto Collection CS5 to be available.
    To enable the Auto Collection CS5 script, choose Edit > Preferences (Windows) or Adobe Bridge CS5.1 > Preferences (Mac OS).
    In the Startup Scripts panel, select Auto Collection CS5, and then click OK.
    Select a folder with the HDR or panoramic shots, and choose Stacks > Auto-Stack Panorama/HDR.
    Choose Tools > Photoshop > Process Collections In Photoshop to automatically merge them and see the result in Adobe Bridge.

  • How to- default to "open all stacks"

    when i import images i set rapid fire pictures to be imported as stacks... i dont' know why, but that's what i've been doing.
    i just noticed when aperture opens it defaults to keeping the stacks closed. this is a problem for me because then i don't realise i have more pictures under the stacks. i just want to see them right away. so i can open all stacks, but is there a way to set aperture so all stacks start off opened?
    thanks,
    max

    You can also use option page down and option page up to skip between stacks, automatically opening them as you go.

  • Collection of stacked images cannot be exported

    I've been thinking my catalog is corrupt for the last five hours, but now I think there's a different problem. My catalog passes integrity checks and can be backed up and optimized and everything - the only problem is with stacking.
    I created a collection, and added all my stacked images to it. I tried exporting the collection as a catalog - fail. I tried selecting all the images in the collection and exporting that - fail. I tried selecting all the images in the collection, switching to "All Photographs" so that I was not in a collection context, and exporting only those selected images - fail. I seem to be able to export any other combination of images and/or collections just fine.
    There's a problem with exporting stacked images, but I'm not sure what it is.

    I had about 250 stacked images that I added to a collection. I expanded all stacks, selected all the stacked images, and a created a collection from the selected images. The following steps are in the original post. I can export one or two stacks here and there, but trying to export all the images in the collection (as a collection or as a 'select all') fails.
    I have my collections set to back up every time I open Lightroom, with verification. I've also optimized the catalog a couple of times. It still doesn't report any errors.
    The system is a MacBook Pro CoreDuo 2.16 GHz, 2 GB RAM, ATI graphics card, OS X Leopard 10.5.6, and Lightroom 2.2.
    Thanks for trying help! I'm at a loss.

  • Why can't I open multiple sparse image files at the same time in FCPX?

    I work in a multiple editor enviroment, where we have hundreds of different projects.  They are all divided into sparse image files to keep them all separated.  I used to be able to mount multiple sparse image files and see them all in FCPx.  But recently, FCPx upon opening, will close out all but one sparse image.  The images are still mounted to the OSx but FCPx will not recognize them.  I can only open one sparse image at a time.  I am needing to export multiple projects at the end of the day, and can't batch export or send them all to compressor because I can open up multiple projects.

    I work in a multiple editor enviroment, where we have hundreds of different projects.  They are all divided into sparse image files to keep them all separated.  I used to be able to mount multiple sparse image files and see them all in FCPx.  But recently, FCPx upon opening, will close out all but one sparse image.  The images are still mounted to the OSx but FCPx will not recognize them.  I can only open one sparse image at a time.  I am needing to export multiple projects at the end of the day, and can't batch export or send them all to compressor because I can open up multiple projects.

  • When I try to open a photoshop image it opens in camera raw

    I store all my images in jpeg.  Been doing my editing elsewhwere, but yesterday tried to use Adobe Bridge.  I opened a jpeg image in camera raw and was unsuccessful in getting what I wanted.  Now, when I try to open one of my jpeg images in Photoshop it opens in camera raw.  If I click on open image it opens, but in a size that is incorrect and is useless.  Help!!!!!!!

    Hope the screenshots will help you.
    On a Mac ACR prefs are in Bridge / Adobe Bridge / Camera Raw Prefs or if you open a file in ACR at the top is a row of icons, if you choose the menu icon it also provides you those prefs.
    I was wrong about PSD, that should have been Tiff btw...

  • I am used to that when I open an image in Bridge it will be opened in PS, with all preferenses I have done to the image. Now it opens in PS but without any changes i have don e in Bridge. Also when I open a new image I want it to be opened in Camera Raw a

    I am used to that when I open an image in Bridge it will be opened in PS, with all preferenses I have done to the image. Now it opens in PS but without any changes i have don e in Bridge. Also when I open a new image I want it to be opened in Camera Raw automatically, both if a Jpeg or Raw picture.
    Using PS CC
    Regards BOJ

    <moved from Adobe Creative Cloud to Bridge General Discussion>

  • Using Lightroom 5.5 and Photoshop CC2014. Images no longer open in Photoshop when using "edit in" command. Photoshop opens but no image when trying to move between LR and PS. Any suggestions?

    Using Lightroom 5.5 and Photoshop CC2014. Images no longer open in Photoshop when using "edit in" command. Photoshop opens but no image when trying to move between LR and PS. Any suggestions?

    1. You have allowed Apple to auto-upgrade your Mac
    Turn off auto-update here:
    Menu > Apple > System Preferences > App Store
    2. The Icons on your dock are Aliases not real apps
    They point to where the apps really are which is:
    For Pages 5.2.2 in your Applications folder
    For Pages '09 in your Applications/iWork folder
    3. You are alternately opening documents randomly with either version of Pages
    Both Pages have the same file extension .pages and there is no certainty as to which version opens them when you double click on a file.
    right click on the file and choose which version you want to open it
    4. Pages '09 can not open Pages 5 files
    Pages 5 can not open Pages '08 files, and will convert and change Pages '09 and Word files.
    It will also auto save opened files into its own format.
    You can export these back to Pages '09 if you need to:
    Menu > File > Export > Pages '09
    5. Yes Pages 5.2.2 is a marked downgrade
    Pages 5.2.2 has a few improvements but has had over 110 features removed and is buggy.
    Sooner or later you will not be able to open a file or have it damaged in some way and it has a complex obscure file format largely incompatible with everything else, so you will not be able to rescue the contents of your file. If Pages or some third party server/eMail don't trash your file, eventually Apple will do it for you as it did when it released Pages 5 last September. I recommend using Pages '09 for the time being whilst you look for viable alternatives, some are here already and some are on the way.
    For further information about what has happened:
    http://www.freeforum101.com/iworktipsntrick/viewforum.php?f=22&sid=0882463378700 abf43a0f2433506bbbc&mforum=iworktipsntrick
    Peter

  • Bridge CS4 has LONG delay in opening the first image

    Photoshop CS4 upgrade was my Christmas present this year. I've been fighting this annoying "problem" ever since then...
    I DO see this "problem" on my desktop PC, which is a Dell XPS-400 PC (with 2 GB of memory) running Windows XP (Media Center Edition) with SP3 installed. I DO NOT see this "problem" on my laptop, which is a Dell XPS-1530 (4 GB of memory) running Windows Vista SP1. I installed the Photoshop CS4 software exactly the same way on both machines, and I have the preferences set the same in both Photoshop and Bridge (and Camera Raw) on both machines.
    Here's the situation: I first open Photoshop CS4 and then click on the Bridge icon in the Application Bar to open Bridge. When I use Bridge to open a photo, by either double-clicking the thumbnail, or right-clicking on the thumbnail and choose "Open" from the context menu, there is a 42 second delay before Photoshop opens the file. This long delay only occurs when opening the very first file.
    Once that first image file is opened, double-clicking any thumbnail in Bridge will have it open in Photoshop CS4 in about 2 seconds. There will never be another long delay in having Bridge pass a file to Photoshop (or Camera Raw) again - until I close the applications and restart them. Once I restart the applications, the first photo takes 42 seconds to open....
    This delay does not occur in opening the first image file if I right-click on the thumbnail in Bridge CS4 and choose "Open With" and manually choose Photoshop CS4.
    Even if that is how I open the first (or several) image file(s), the first time I try to open a file from Bridge by double-clicking on a thumbnail (or right-click on a thumbnail and choose "Open") there will be that annoying 42 second delay before it opens.
    It does not matter what the file format the first image file is (JPG, PSD, TIFF, or DNG), or what the file format of any subsequent image file is. As long as I do not close the Bridge and Photoshop applications, any subsequent file will be passed from Bridge to Photoshop in only a couple of seconds.
    I have manually set the File Name Extensions in Windows XP, and in the Preferences in Bridge. Both have been set to open the file types listed above with Photoshop CS4.
    I have uninstalled CS4, and have used two seperate Registry cleaners (CCleaner and jv16 Power Tools) before re-installing Photoshop CS4. This had no effect on this situation. I've run "chkdsk C: /r" several times, with no problems reported.
    I have been searching through these forums for over 2 weeks now, and I have not seen anyone else report such a problem. I use my XP desktop much more than my Vista laptop, so I'd really like to fix this situation, but I don't know what else to try.
    Gregg Mack

    Don,
    Thanks for all of your suggestions. I tried them all, but the problem remains exactly as it was. To properly document my efforts:
    In Bridge's Preferences, I Purged and Compacted the Bridge Cache, then changed it's location to D:\Bridge_Cache (D:\ is a second physical internal SATA drive).
    I can not tell the exact size the Cache is set to, but the slider in Bridge's Preference is very close to the left end (10,000) of the slider.
    The Windows Page File is set to 3072 MB min and 4096 max, and it is entirely on the D:\ drive. (I have 2GB of physical RAM in the PC.)
    I defragmented the C:\ drive using Diskeeper 2008 Pro Premier, and even ran a Boot Time Defrag.
    Rather than set some exclusions for Norton Anti-Virus, I jsut disbled that Virus checking program for all of my experiments.
    I deleted the Bridge Preference File by holding down the Ctrl key as Bridge was restarted.
    I even deleted the entire contents of the C:\Windows\Prefetch folder. I then rebooted the PC - twice. I then re-disabled Norton Anti-Virus.
    The PC is approaching 3 years of age, but it is a 3.2 GHz Pentium D machine with 2 GB of RAM and two internal SATA drives. Every other application that I run on this machine responds reponsively. Again it is only the FIRST image file that I have Bridge hand off to Photoshop (or Camera Raw) that takes forever. The second and subsequent image files take a second or two.... That doesn't sound like it's an "old hardware" problem to me.
    I'm willing to try anything else that you, or anyone else would like to suggest.
    Thanks
    Gregg Mack

  • I own a Canon 6D and just bought Photoshop CS6 and I am not able to open my raw images into Photoshop CS6. What do I do to fix this?

    I own a Canon 6D and just bought Photoshop CS6 and I am not able to open my raw images into Photoshop CS6. I downloaded the camera raw and dng converter for it, but realized in the process that the one I downloaded does not work with my Mac version, 10.9.5.

    Camera Raw plug-in | Supported cameras
    Camera Raw-compatible Adobe applications
    Mylenium

  • How do I open a raw image with the Photoshop raw plug in as opposed to the Bridge raw plug-in.

    I read in a book on adobe raw that it is often useful to open an image at the same time with the adobe camera raw bridge plug in and the Photoshop camera raw plug in.
    I can open a raw image in photoshop but I suspect I am not actually getting access to the camera raw plug in as none of the controls present in the bridge raw plug seem to be available from within Photoshop.
    Of course I can access bridge and the bridge raw plug in by opening bridge from within Photoshop but this is not what I want to do.  I would like to open the image using the photoshop raw plug in not the bridge plug in.
    Clueless . . . and confused.
    --Kenoli

    Thanks for the discussion.  It is interesting.  Let me clarify a bit regarding my issue.
    I am using Mountain Lion OSX on a mac, of course, and CS6.  I have been using Aperture, a piece of Apple Software similar to Light Room to organize my images, opening them from Aperture in Photoshop to edit them, as I am both familiar with Photoshop and like the way it does things better than Aperture.  I recently started using CS6 and working with Adobe Camera raw 7, which I think is the version that comes with CS6.  All the info I can get from the web site, including a very nice tutorial from Adobe on camera raw, simply tells me to open it from Bridge.  When I do this, I get a nice set of sliders and other adjustments specifically associated with Adobe Camera Raw and the camera I am using.
    I can open a file in Photoshop using the method SkillRooster suggests and, sure enough, it opens it with the camera raw plug-in (if I simply open the image by double clicking on it it opens in photoshop, no plug-in).  If I then go to bridge and open it from there, I don't get a second instance of Camera raw, it simply points me at the instance opened through Photoshop.
    However, when I open a raw image in Photoshop from Aperture  (raw images open with no problem) I simply get the Photoshop interface, not the camera raw plug-in, the same as if I had double clicked on the image to open it from outside of Aperture.  I am trying to figure out if there is some way to open an image from Aperture in Photoshop so that it opens in the camera raw plug-in.  One possibility I could imagene is to open it in Photoshop and from there open it in the plug-in.  The only thing I see regarding this in Photoshop is a menu item that lets me close the image and open Bridge, which doesn't help me with my Aperture issue.  I could decide to switch to bridge, but with the thousands of images I now have in Aperture, this would be quite a bit of work.  I may just have to work with both going forward.
    The root of my original question comes from something I recently read in a book by Bruce Fraser on Camera Raw which is excellent, but it focues on CS 5.5 as he died before being able to update it.  In that book he describes a trick he uses where he opens the raw image in a plug-in in Bridge and then opens it a second time using a plug-in in Photoshop.  This give him a chance to compare adjustments between the two open images.  As I mentioned above, when I try to do this by starting with Photoshop and then going to Bridge, it points me at the same instance.  I can't open it in Bridge and then Photoshop since once it is open in Bridge, it won't let me into Photoshop without closing the image in Bridge.  I was thinking there might be something in Fraser's method that would help me with my Aperture issue, but can't reproduce what he describes.
    Perhaps this was possible in CS5.5 but no longer  in CS6.
    Another work around I can imagine is to do all my raw editing from Bridge and then save the file as a DNG file in Aperture.  I suspect that after that, I am stuck with doing any more raw editing using the Aperture camera raw funcions, which are a bit lacking compared with Adobe Camera Raw.
    Hope I am being clear here about my dilemma.  Any help would be welcomed.
    --Kenoli

  • I recently purchased a Canon 7D. I own Adobe Photoshop/Bridge CS5. I cannot open my raw images in Bridge. I have tried to download the plug in but does not seem to work. Please Help, I need to be able to open my raw images in Bridge ASAP. I do not want to

    I recently purchased a Canon 7D. I own Adobe Photoshop/Bridge CS5. I cannot open my raw images in Bridge. I have tried to download the plug in but does not seem to work. Please Help, I need to be able to open my raw images in Bridge ASAP. I do not want to upgrade to CS6 at this time.

    If you had given us sensible information, I could look it up for you if your efforts fail.
    Right now, I don't even know if you are on a Mac or on a Windows box.
    BOILERPLATE TEXT:
    If you give complete and detailed information about your setup and the issue at hand, such as your platform (Mac or Win), exact versions of your OS, of Photoshop and of Bridge, machine specs, what troubleshooting steps you have taken so far, what error message(s) you receive, if having issues opening raw files also the exact camera make and model that generated them, etc., someone may be able to help you.
    Please read this FAQ for advice on how to ask your questions correctly for quicker and better answers:
    http://forums.adobe.com/thread/419981?tstart=0
    Thanks!

  • I can not open a crw image in photoshop camera Raw.

    When I go to open a CRW Image in CS5,Bridge It will not open.It says Could not complite your request because it is not the right kind of document.Need help bad.
    PS How do I tell what version of Camera Raw I have.By the way I have a Canon EOS 10D camera.Thanks.

    Within Photoshop go to the "About Plug-in…" menu item just below "About Photoshop" to find the Camera Raw version number.  On which menu that is depends on your platform, Macintosh or Windows, which you neglected to mention.
    Raw files from your camera have been supported since version 2.0 of Camera Raw for years and years, so it's not a question of your version of ACR.  Any version of ACR that runs in CS5 should open those files.
    I suspect your raw files are damaged (corrupted).

  • Cannot open camera RAW images from Sony DSC-RX100M3 camera.  Working on a Mac in Photoshop CS5 and have camera raw 6.7.

    Cannot open camera RAW images from Sony DSC-RX100M3 camera.  Working on a Mac with Photoshop CS5 and Camera Raw 6.7?

    Bruce,
    When I made the transition to digital some 8 years ago, I had tremendous help from a number of well documented websites, among which:
    http://www.luminous-landscape.com
    I think a lot of stuff there to get you seriously going. Another one is:
    http://www.computer-darkroom.com
    I sold all my film based stuff, except a Nikon F3 and a handful of lenses and a Paterson developing tank.
    The Nikon suspiciously smells like foam mirror damping strips chemically decaying.
    I sold my enlarger over the internet. The word "enlarger" caused me to be on SpamCops blacklist for a while.
    I'm in this since the seventies, and I think you'll be as amazed as I was at the possibilities and control you have. And no more bags with $300 worth of film that's consumed in one shoot.
    Jump in both feet! you won't be sorry. And these forums are the best help you can get.
    Good luck,
    Rob

Maybe you are looking for

  • BUG: Entering a "version" when deploying to a WebLogic server doesn't work

    By default when deploying to a weblogic server the "Version" is set to v2.0. If you change that to something like v2.1 when the application is deployed, the deployment logs still show the Version=2.0. What needs to be done to get the Version in deplo

  • Samsung 6400 LED TV, 2nd Generation Apple TV, HDMI, only 780...

    I have a 2nd generation apple TV connected to my brand new Samsung 6400 LED via HDMI and am only getting 780 screen resolution.  My other devices, all connected via HDMI, are showing in 1080.  I have a 1st gen apple TV in my bedroom, connected to a s

  • Problem while instantiating

    I simply wrote this 2 lines of code: import flash.display.DisplayObject; var testIt:DisplayObject = new DisplayObject(); And I receive this weird error: ArgumentError: Error #2012: DisplayObject$ class cannot be instantiated. Any idea? Thanks in adva

  • Cannot stop users disabling WiFi

    Users who are not local administrators and via the control panel cannot do so can disable the WiFi via the sidebar BS in Windows 8.1. This is costing us large amounts of time supporting customers and talking through remotely re-enabling or leading to

  • Error in Interactive form

    Trying to explore interactive forms on ECC 5.0 as very new to this field. Used T-code 'SFP' to view the standard Form 'MEDRUCK_PO'. When executing, during print previw provided the the default printer name in out put device but got following Error me