opening MicroManager files query
Locked
opening MicroManager files query
 
|
Is there a package of plugins or macros for opening MM files and sorting them into stacks or hyperstacks?
In our lab users are beginning to use MM to collect tiles or multiple positions with multiple channels sometimes as Z series or time series and I've been writing macros on an ad hoc basis per each user's experimental conditions but realize there must be a better way to do this. Thanks!! ________________________________________________________ Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine Lab: (212) 263-3208 Cell: (914) 309-3270 </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE> |
|
Hi Michael,
Is there a package of plugins or macros for opening MM files and sorting > them into stacks or hyperstacks? > Bio-Formats supports the Micro-Manager format. Please let us know if you have any problems with it. Regards, Curtis On Wed, Nov 16, 2011 at 11:36 AM, Cammer, Michael < [hidden email]> wrote: > Is there a package of plugins or macros for opening MM files and sorting > them into stacks or hyperstacks? > > In our lab users are beginning to use MM to collect tiles or multiple > positions with multiple channels sometimes as Z series or time series and > I've been writing macros on an ad hoc basis per each user's experimental > conditions but realize there must be a better way to do this. > > Thanks!! > > > ________________________________________________________ > Michael Cammer, Assistant Research Scientist > Skirball Institute of Biomolecular Medicine > Lab: (212) 263-3208 Cell: (914) 309-3270 > > </PRE> > <html> > <body> > ------------------------------------------------------------<br /> > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email.<br /> > ================================= > </body> > </html> > <PRE> > |
|
|
Hi Michael,
How do I select a folder to open in the Bio-Formats? For instance, if I > have a folder named "KO" and in it there are a bunch of folders called > "5-Pos_###_###" each with four channels in it, and I want to open each set > of channels into a stack, how do I do this with LOCI? > Hmm, maybe the Micro-Manager format has changed again? Did you try selecting the metadata.txt file? (There is such a file, right?) What version of Micro-Manager are you running? Regards, Curtis On Wed, Nov 16, 2011 at 1:15 PM, Cammer, Michael <[hidden email] > wrote: > Thanks for the reply. > > How do I select a folder to open in the Bio-Formats? For instance, if I > have a folder named "KO" and in it there are a bunch of folders called > "5-Pos_###_###" each with four channels in it, and I want to open each set > of channels into a stack, how do I do this with LOCI? > > Regards, > > Michael > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Curtis Rueden > Sent: Wednesday, November 16, 2011 1:36 PM > To: [hidden email] > Subject: Re: opening MicroManager files query > > Hi Michael, > > Is there a package of plugins or macros for opening MM files and sorting > > them into stacks or hyperstacks? > > > > Bio-Formats supports the Micro-Manager format. Please let us know if you > have any problems with it. > > Regards, > Curtis > > > On Wed, Nov 16, 2011 at 11:36 AM, Cammer, Michael < > [hidden email]> wrote: > > > Is there a package of plugins or macros for opening MM files and sorting > > them into stacks or hyperstacks? > > > > In our lab users are beginning to use MM to collect tiles or multiple > > positions with multiple channels sometimes as Z series or time series > and > > I've been writing macros on an ad hoc basis per each user's experimental > > conditions but realize there must be a better way to do this. > > > > Thanks!! > > > > > > ________________________________________________________ > > Michael Cammer, Assistant Research Scientist > > Skirball Institute of Biomolecular Medicine > > Lab: (212) 263-3208 Cell: (914) 309-3270 > > > > </PRE> > > <html> > > <body> > > ------------------------------------------------------------<br /> > > This email message, including any attachments, is for the sole use of the > > intended recipient(s) and may contain information that is proprietary, > > confidential, and exempt from disclosure under applicable law. Any > > unauthorized review, use, disclosure, or distribution is prohibited. If > you > > have received this email in error please notify the sender by return > > and delete the original message. Please note, the recipient should check > > this email and any attachments for the presence of viruses. The > > organization accepts no liability for any damage caused by any virus > > transmitted by this email.<br /> > > ================================= > > </body> > > </html> > > <PRE> > > > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > ================================= > > |
|
|
Hi Michael,
I just installed Latest Version: 4.3.3 (2011 October 18) which does allow > me to click on the metadata file, but this only opens the images in that > directory. The problem is that when imaging multiple stage positions, each > position is in a separate folder as per the attached pic. > OK, thanks for the explanation. Presumably Micro-Manager does not include any sort of metadata file in the toplevel directory? We want to open each channel and make a stack to then make a mosaic. I > have a macro where we code in the filenames and the user selects the parent > directory, but it would be nice to have this as a more user friendly > method. I could probably do this as a macro, but I don't want to reinvent > the wheel. > Unfortunately, I think the wheel has yet to be invented on this one. Unless someone else out there has already done it? Anyway, if you write a working macro, it would be very nice to post here and/or send to the Micro-Manager team, so that others can make use of it too! Regards, Curtis On Wed, Nov 16, 2011 at 2:07 PM, Cammer, Michael <[hidden email] > wrote: > Curtis,**** > > I just installed Latest Version: 4.3.3 (2011 October 18) which does allow > me to click on the metadata file, but this only opens the images in that > directory. The problem is that when imaging multiple stage positions, each > position is in a separate folder as per the attached pic. We want to open > each channel and make a stack to then make a mosaic. I have a macro where > we code in the filenames and the user selects the parent directory, but it > would be nice to have this as a more user friendly method. I could > probably do this as a macro, but I don't want to reinvent the wheel.**** > > Regards,**** > > Michael**** > > ** ** > > *From:* [hidden email] [mailto:[hidden email]] *On > Behalf Of *Curtis Rueden > *Sent:* Wednesday, November 16, 2011 2:37 PM > *To:* ImageJ Interest Group > *Cc:* Cammer, Michael > > *Subject:* Re: opening MicroManager files query**** > > ** ** > > Hi Michael,**** > > How do I select a folder to open in the Bio-Formats? For instance, if I > have a folder named "KO" and in it there are a bunch of folders called > "5-Pos_###_###" each with four channels in it, and I want to open each set > of channels into a stack, how do I do this with LOCI?**** > > > Hmm, maybe the Micro-Manager format has changed again? Did you try > selecting the metadata.txt file? (There is such a file, right?) What > version of Micro-Manager are you running? > > Regards, > Curtis > > **** > > On Wed, Nov 16, 2011 at 1:15 PM, Cammer, Michael < > [hidden email]> wrote:**** > > Thanks for the reply. > > How do I select a folder to open in the Bio-Formats? For instance, if I > have a folder named "KO" and in it there are a bunch of folders called > "5-Pos_###_###" each with four channels in it, and I want to open each set > of channels into a stack, how do I do this with LOCI? > > Regards, > > Michael**** > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Curtis Rueden > Sent: Wednesday, November 16, 2011 1:36 PM > To: [hidden email] > Subject: Re: opening MicroManager files query > > Hi Michael, > > Is there a package of plugins or macros for opening MM files and sorting > > them into stacks or hyperstacks? > > > > Bio-Formats supports the Micro-Manager format. Please let us know if you > have any problems with it. > > Regards, > Curtis > > > On Wed, Nov 16, 2011 at 11:36 AM, Cammer, Michael < > [hidden email]> wrote: > > > Is there a package of plugins or macros for opening MM files and sorting > > them into stacks or hyperstacks? > > > > In our lab users are beginning to use MM to collect tiles or multiple > > positions with multiple channels sometimes as Z series or time series > and > > I've been writing macros on an ad hoc basis per each user's experimental > > conditions but realize there must be a better way to do this. > > > > Thanks!! > > > > > > ________________________________________________________ > > Michael Cammer, Assistant Research Scientist > > Skirball Institute of Biomolecular Medicine > > Lab: (212) 263-3208 Cell: (914) 309-3270 > > > > </PRE> > > <html> > > <body> > > ------------------------------------------------------------<br /> > > This email message, including any attachments, is for the sole use of the > > intended recipient(s) and may contain information that is proprietary, > > confidential, and exempt from disclosure under applicable law. Any > > unauthorized review, use, disclosure, or distribution is prohibited. If > you > > have received this email in error please notify the sender by return > > and delete the original message. Please note, the recipient should check > > this email and any attachments for the presence of viruses. The > > organization accepts no liability for any damage caused by any virus > > transmitted by this email.<br /> > > ================================= > > </body> > > </html> > > <PRE> > >**** > > ------------------------------------------------------------**** > > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email.**** > > =================================**** > > ** ** > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > ================================= > > |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |