look for the difference

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look for the difference

pierre.bourdoncle@inserm.fr
Dear ImageJ community

I currently have problems opening some image formats like the .tif of
the attached HCImageLive (Hamamatsu) software and the GSD (Leica) .lif.
I can open them with FIJI and LOCI but never with ImageJ and LOCI.
I attach a screenshot for the ImageJ error message and the difference
between ImageJ and FIJI.
Thank you for your answers

--

*/-------------------
/**/Pierre Bourdoncle
/*Plate-forme IMAG'IC
Institut Cochin
Inserm U1016-CNRS UMR8104-Université Paris Descartes

bât. Roussy 5ème étage

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Tel.33(0)1 40 51 65 84 – Fax 33(0)1 40 51 65 35*
www.institutcochin.fr
#InstitutCochin*

Plate-Forme IMAG'IC
<http://www.institutcochin.fr/les-plateformes/microscopie-photonique>

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flash-code-logo-ic imagic.jpg (74K) Download Attachment
screen ImageJ FIJI.jpg (971K) Download Attachment
Image151.tif (2M) Download Attachment
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Re: look for the difference

Gabriel Landini
I can open the tif file in IJ.
Did you check that you have the latest loci version?

Cheers

Gabriel


On Tuesday, 2 October 2018 10:23:57 BST you wrote:
> Dear ImageJ community
>
> I currently have problems opening some image formats like the .tif of
> the attached HCImageLive (Hamamatsu) software and the GSD (Leica) .lif.
> I can open them with FIJI and LOCI but never with ImageJ and LOCI.
> I attach a screenshot for the ImageJ error message and the difference
> between ImageJ and FIJI.
> Thank you for your answers

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Re: look for the difference

pierre.bourdoncle@inserm.fr
yes I have the trunk build


Le 02/10/2018 à 11:40, Gabriel Landini a écrit :

> I can open the tif file in IJ.
> Did you check that you have the latest loci version?
>
> Cheers
>
> Gabriel
>
>
> On Tuesday, 2 October 2018 10:23:57 BST you wrote:
>> Dear ImageJ community
>>
>> I currently have problems opening some image formats like the .tif of
>> the attached HCImageLive (Hamamatsu) software and the GSD (Leica) .lif.
>> I can open them with FIJI and LOCI but never with ImageJ and LOCI.
>> I attach a screenshot for the ImageJ error message and the difference
>> between ImageJ and FIJI.
>> Thank you for your answers
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

*/-------------------
/**/Pierre Bourdoncle
/*Plate-forme IMAG'IC
Institut Cochin
Inserm U1016-CNRS UMR8104-Université Paris Descartes

bât. Roussy 5ème étage

8 rue Méchain, 75014 Paris
Tel.33(0)1 40 51 65 84 – Fax 33(0)1 40 51 65 35*
www.institutcochin.fr
#InstitutCochin*

Plate-Forme IMAG'IC
<http://www.institutcochin.fr/les-plateformes/microscopie-photonique>

********************************
Ce message et toutes les pièces jointes (ci-après le "message") sont
confidentiels et établis à l'intention exclusive de ses destinataires.
Toute utilisation ou diffusion non autorisée est interdite.
Tout message électronique est susceptible d'altération. L’Institut
Cochin décline toute responsabilité au titre de ce message s'il a été
altéré, déformé ou falsifié.
Si vous n'êtes pas destinataire de ce message, merci de le détruire
immédiatement et d'avertir l'expéditeur.

*********************************
This message and any attachments (the "message") are confidential and
intended solely for the addressees.
Any unauthorised use or dissemination is prohibited.
Messages are susceptible to alteration. Cochin Institute shall not be
liable for the message if altered, changed or falsified.
If you are not the intended addressee of this message, please cancel it
immediately and inform the sender.

********************************




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flash-code-logo-ic imagic.jpg (74K) Download Attachment
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Re: look for the difference

Herbie
In reply to this post by pierre.bourdoncle@inserm.fr
Good day,

the TIF-file is opened directly by plain ImageJ, i.e. without using
BioFormats.

(macOS 10.11.6, ImageJ 1.52g, Java 1.8.0_172)

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::



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extending the range allowed within B&C

Jeremy Adler
In reply to this post by pierre.bourdoncle@inserm.fr
I have an RGB image where I want to reduce the intensity of one channel, which basically shows the area of a cell, relative to the other channels whose information is of more interest

The obvious way would be to increase the Maximum display intensity for this channel  e.g. if the most intense pixels is 128, to make the full scale 255. But the selectable range for the Maximum slider is limited to the max intensity in the channel, so this does not work. Increasing the Minimum does reduce the display of intermediate intensities but then the lower intensities disappear from the display and the limits of the cell are no longer apparent.


Would it be possible to alter the B&C to allow a Maximum to set that exceeds the maximum intensity in the channel. There are also cases when allowing a Minimum that is lower than the min intensity in the channel would be useful.


I could write a macro or game the B&C by changing single pixel in one channel to the Maximum I want to use for the channel but it would be simpler for users if, within B&C, the Max and Min sliders were allowed to exceed the range of intensities present in the image. To make it apparent that the display range exceeds the intensity range in the image, the number shown by the B&C might be switched to red.

In addition a log histogram option for B&C and thresholding would be helpful.


Jeremy Adler

BioVis

Uppsala U






















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Re: extending the range allowed within B&C

Herbie
Good day Jeremy,

you can numerically *Set* a higher value, e.g. 511 for an 8bit image.

HTH

Herbie

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Re: look for the difference

pierre.bourdoncle@inserm.fr
In reply to this post by Herbie
I just understood the problem, I used the 'Update Bio-Formats Plugins'
directly from the plugin. And he gave me a bad version of LOCI.

I directly loaded the plugin on the site:
http://www.openmicroscopy.org/bio-formats/downloads/ and there it is good.

it must be the plugin that targets badly.


Thank you all for your responses

Pierre


Le 02/10/2018 à 12:47, Herbie a écrit :

> Good day,
>
> the TIF-file is opened directly by plain ImageJ, i.e. without using
> BioFormats.
>
> (macOS 10.11.6, ImageJ 1.52g, Java 1.8.0_172)
>
> Regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::::::::::::::::
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


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