Exporting 8 bits color .tif images in Cell Sens

[jlribas]

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Dear Coleagues,
Last year we upgraded our BX61 with CellSens software and a new DP73
camera. Almost all of our users wants to get multichannel 8 bits color
images in ".tif" format and the software cannot get them without
exporting each channel separately, which is very time consuming.
Multichannel acquisition does not work in 8 bits mode. In my opinion it
should be a decision of the user to work with 8 or 16 bits acquisition
and also with gray or color images.
As an alternative, I've tried to configure a 8 bits multichannel color
acquisition with Experiment Manager but the system produce 3 separated
.vsi images for each channel and you have to go one by one converting
".vsi" to ".tif" format.
I wonder if someone has an alternative way to acquire quickly (one mouse
click) multichannel 8 bit color images and generate ".tif" images for
each channel?

Thank you very much in advance.

All the best
Juan Luis Ribas
--
Juan Luis Ribas
Servicio de Microscopía
Centro de Investigación, Tecnología e Innovación
Universidad de Sevilla
Av. Reina Mercedes 4b
41012 Sevilla

Tfnos: 954559983 // 628220681 // 12068

http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento

[Sathya]

Hi Juan,
Have you tried the following in CellSens:

select Image>Mode>8 bit/Channel menu command to change the image into 8�\bit
image. Use File>Save as… menu command to save the image as one image containing multiple channels or use
File>Export to>tiff series… command to save the image as multiple images for each channel

I do not have access to CellSens right now. I had this notes which I have collected from some web site with me and thought of sharing it with you. Good luck.

Sathya Srinivasan

________________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Juan Luis Ribas <[hidden email]>
Sent: December 15, 2015 7:09 AM
To: [hidden email]
Subject: Exporting 8 bits color .tif images in Cell Sens

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Dear Coleagues,
Last year we upgraded our BX61 with CellSens software and a new DP73
camera. Almost all of our users wants to get multichannel 8 bits color
images in ".tif" format and the software cannot get them without
exporting each channel separately, which is very time consuming.
Multichannel acquisition does not work in 8 bits mode. In my opinion it
should be a decision of the user to work with 8 or 16 bits acquisition
and also with gray or color images.
As an alternative, I've tried to configure a 8 bits multichannel color
acquisition with Experiment Manager but the system produce 3 separated
.vsi images for each channel and you have to go one by one converting
".vsi" to ".tif" format.
I wonder if someone has an alternative way to acquire quickly (one mouse
click) multichannel 8 bit color images and generate ".tif" images for
each channel?

Thank you very much in advance.

All the best
Juan Luis Ribas
--
Juan Luis Ribas
Servicio de Microscopía
Centro de Investigación, Tecnología e Innovación
Universidad de Sevilla
Av. Reina Mercedes 4b
41012 Sevilla

Tfnos: 954559983 // 628220681 // 12068

http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento

[jlribas]

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Thank you for all the people that reply, but unfortunately I have to say
that at the end all the procedures finished in gray scale images .tif
images.
Definitevely, it should be named CellNoSens or Cell-nonSens. I wonder if
the vendor could argue something about this question. About 50 users in
my facility moved to another microscope beside. The companies has to
design the software to do the life easier...
On the other hand, perhaps some expert in ImageJ could know if there is
a plugin in ImageJ that could convert .vsi files to .tif 8 bit color .

Best regards
Juan Luis Ribas

El 16/12/2015 a las 2:09, Sathya Srinivasan escribió:

> Hi Juan,
> Have you tried the following in CellSens:
>
> select Image>Mode>8 bit/Channel menu command to change the image into 8‐bit
> image. Use File>Save as… menu command to save the image as one image containing multiple channels or use
> File>Export to>tiff series… command to save the image as multiple images for each channel
>
> I do not have access to CellSens right now. I had this notes which I have collected from some web site with me and thought of sharing it with you. Good luck.
>
> Sathya Srinivasan
>
> ________________________________________
> From: Confocal Microscopy List <[hidden email]> on behalf of Juan Luis Ribas <[hidden email]>
> Sent: December 15, 2015 7:09 AM
> To: [hidden email]
> Subject: Exporting 8 bits color .tif images in Cell Sens
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear Coleagues,
> Last year we upgraded our BX61 with CellSens software and a new DP73
> camera. Almost all of our users wants to get multichannel 8 bits color
> images in ".tif" format and the software cannot get them without
> exporting each channel separately, which is very time consuming.
> Multichannel acquisition does not work in 8 bits mode. In my opinion it
> should be a decision of the user to work with 8 or 16 bits acquisition
> and also with gray or color images.
> As an alternative, I've tried to configure a 8 bits multichannel color
> acquisition with Experiment Manager but the system produce 3 separated
> .vsi images for each channel and you have to go one by one converting
> ".vsi" to ".tif" format.
> I wonder if someone has an alternative way to acquire quickly (one mouse
> click) multichannel 8 bit color images and generate ".tif" images for
> each channel?
>
> Thank you very much in advance.
>
> All the best
> Juan Luis Ribas
> --
> Juan Luis Ribas
> Servicio de Microscopía
> Centro de Investigación, Tecnología e Innovación
> Universidad de Sevilla
> Av. Reina Mercedes 4b
> 41012 Sevilla
>
> Tfnos: 954559983 // 628220681 // 12068
>
> http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento

--
Juan Luis Ribas
Servicio de Microscopía
Centro de Investigación, Tecnología e Innovación
Universidad de Sevilla
Av. Reina Mercedes 4b
41012 Sevilla

Tfnos: 954559983 // 628220681 // 12068

http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento

[Ondřej Šebesta]

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*****

Hello Juan

Despite you are absolutely right, that Olympus should improve export
capabilities of IMHO any of their software, ImageJ is surely able to
convert many formats. I do not have personal experience with .vsi files,
but I guess Bioformats would import correctly and resave is easy. You can
use a macro recorder to get a primitive macro which can do the job for you.
Batch process - macro is another usefull tool.

Best, Ondrej Sebesta

2015-12-16 14:42 GMT+01:00 Juan Luis Ribas <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Thank you for all the people that reply, but unfortunately I have to say
> that at the end all the procedures finished in gray scale images .tif
> images.
> Definitevely, it should be named CellNoSens or Cell-nonSens. I wonder if
> the vendor could argue something about this question. About 50 users in my
> facility moved to another microscope beside. The companies has to design
> the software to do the life easier...
> On the other hand, perhaps some expert in ImageJ could know if there is a
> plugin in ImageJ that could convert .vsi files to .tif 8 bit color .
>
> Best regards
> Juan Luis Ribas
>
>
> El 16/12/2015 a las 2:09, Sathya Srinivasan escribió:
>
>> Hi Juan,
>> Have you tried the following in CellSens:
>>
>> select Image>Mode>8 bit/Channel menu command to change the image into
>> 8‐bit
>> image. Use File>Save as… menu command to save the image as one image
>> containing multiple channels or use
>> File>Export to>tiff series… command to save the image as multiple images
>> for each channel
>>
>> I do not have access to CellSens right now. I had this notes which I have
>> collected from some web site with me and thought of sharing it with you.
>> Good luck.
>>
>> Sathya Srinivasan
>>
>> ________________________________________
>> From: Confocal Microscopy List <[hidden email]> on
>> behalf of Juan Luis Ribas <[hidden email]>
>> Sent: December 15, 2015 7:09 AM
>> To: [hidden email]
>> Subject: Exporting 8 bits color .tif images in Cell Sens
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Dear Coleagues,
>> Last year we upgraded our BX61 with CellSens software and a new DP73
>> camera. Almost all of our users wants to get multichannel 8 bits color
>> images in ".tif" format and the software cannot get them without
>> exporting each channel separately, which is very time consuming.
>> Multichannel acquisition does not work in 8 bits mode. In my opinion it
>> should be a decision of the user to work with 8 or 16 bits acquisition
>> and also with gray or color images.
>> As an alternative, I've tried to configure a 8 bits multichannel color
>> acquisition with Experiment Manager but the system produce 3 separated
>> .vsi images for each channel and you have to go one by one converting
>> ".vsi" to ".tif" format.
>> I wonder if someone has an alternative way to acquire quickly (one mouse
>> click) multichannel 8 bit color images and generate ".tif" images for
>> each channel?
>>
>> Thank you very much in advance.
>>
>> All the best
>> Juan Luis Ribas
>> --
>> Juan Luis Ribas
>> Servicio de Microscopía
>> Centro de Investigación, Tecnología e Innovación
>> Universidad de Sevilla
>> Av. Reina Mercedes 4b
>> 41012 Sevilla
>>
>> Tfnos: 954559983 // 628220681 // 12068
>>
>> http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento
>>
>
> --
> Juan Luis Ribas
> Servicio de Microscopía
> Centro de Investigación, Tecnología e Innovación
> Universidad de Sevilla
> Av. Reina Mercedes 4b
> 41012 Sevilla
>
> Tfnos: 954559983 // 628220681 // 12068
>
> http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento
>
> --
> <http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento>
> Mgr. Ondřej Šebesta
> E-mail:
> <http://investigacion.us.es/scisi/sgi/servicios/microscopia/equipamiento>
> [hidden email]
>
> Univerzita Karlova v Praze
> Přírodovědecká fakulta
> Albertov 6, 128 43 Praha 2
> www.natur.cuni.cz
>
> Charles University in Prague
> Faculty of Science
> Albertov 6, 128 43 Praha 2
> www.natur.cuni.cz/en
>
>

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