[ome-users] photoconversion of td-Tomato in diaminobenzidine

Fri Mar 20 13:06:25 GMT 2015

Does anyone know of a reliable method for photoconverting td-Tomato to an osmiophilic substance for electron microscopy?

-----Original Message-----
From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of ome-users-request at lists.openmicroscopy.org.uk
Sent: Friday, March 20, 2015 7:00 AM
To: ome-users at lists.openmicroscopy.org.uk
Subject: ome-users Digest, Vol 120, Issue 17

Send ome-users mailing list submissions to
	ome-users at lists.openmicroscopy.org.uk

To subscribe or unsubscribe via the World Wide Web, visit
	https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicroscopy.org.uk_mailman_listinfo_ome-2Dusers&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=RXuc9hqsfNP634tZ5Rev-WW0RWNmBMarOaHF_vNIBTE&e=
or, via email, send a message with subject or body 'help' to
	ome-users-request at lists.openmicroscopy.org.uk

You can reach the person managing the list at
	ome-users-owner at lists.openmicroscopy.org.uk

When replying, please edit your Subject line so it is more specific than "Re: Contents of ome-users digest..."

Today's Topics:

   1. Re: MetaXpress image has cropped metadata values (with	fix)
      (Sebastien Besson)

----------------------------------------------------------------------

Message: 1
Date: Fri, 20 Mar 2015 11:33:00 +0000
From: Sebastien Besson <seb.besson at gmail.com>
To: "ome-users at lists.openmicroscopy.org.uk OME-users"
	<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] MetaXpress image has cropped metadata values
	(with	fix)
Message-ID: <3552BF4B-B3DA-4AEC-B891-3E066665ADD6 at gmail.com>
Content-Type: text/plain; charset=utf-8

Dear Mario,

this looks like the same underlying issue as the one you reported a month ago in https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicroscopy.org.uk_pipermail_ome-2Dusers_2015-2DFebruary_005037.html&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=JlcdKpZcN4KEeemQ9kBfOok0LxhU2Z90NWIqzwtvs-c&e= 

Roger had opened a Pull Request to fix this bug and this change got merged into the 5.1 development line - see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_openmicroscopy_bioformats_pull_1584&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=IpDEE4yNM0ZWQ5eRccHTarrojTxMONv1643fmTApbfc&e= .

I retested the sample file you sent using the last development milestone of Bio-Formats 5.1.x https://urldefense.proofpoint.com/v2/url?u=http-3A__downloads.openmicroscopy.org_bio-2Dformats_5.1.0-2Dm4_&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=_h1ksVieGRSqeUQ-jkQrOsodOQosllhVBobGHJxHaxc&e=  and the metadata should be correctly read by the upcoming 5.1.0 release of Bio-Formats:

$ ./bftools/showinf -version
Version: 5.1.0-m4
VCS revision: 51bf71d
Build date: 19 February 2015
$ ./bftools/showinf b0BCDSL-T069_wG06_s6_z0_t1_cCy5_u001.tif | grep Experiment Experiment base name: SL-HeLa4channels Experiment set: SL-HeLa4channels

Best regards,
Sebastien

> On 20 Mar 2015, at 10:55, Mario Emmenlauer <mario at emmenlauer.de> wrote:
> 
> 
> Dear Bio-Formats developers,
> 
> I have a small issue with MetaXpress meta data. When I read the image 
> (link below), several metadata values are missing their first character.
> An example is 'Experiment base name' for which I expect to get 
> 'SL-HeLa4channels', instead I receive 'L-HeLa4channels'. I could 
> identify in 
> components/formats-gpl/src/loci/formats/in/MetamorphReader.java the 
> code expects always a dummy character after the colon, however in my case I think this dummy is missing. Here a proposed fix:
> 
> -          String value = line.substring(colon + 2);
> +          // Mario Emmenlauer, 2015.03.20: There is not always a space after
> +          // the colon, so better use 'trim()' instead of expecting a space:
> +          String value = line.substring(colon + 1).trim();
> 
> I did not extensively check this fix, so maybe use it with a bit of 
> caution. The image I used is here:
>    
> https://urldefense.proofpoint.com/v2/url?u=http-3A__data.marssoft.de_b
> 0BCDSL-2DT069-5FwG06-5Fs6-5Fz0-5Ft1-5FcCy5-5Fu001.tif&d=AwICAg&c=6vgNT
> iRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK
> -dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=ohLqbhg
> p-sr7LQA5l4Jswa4qqpdu2lgO2O8ufND59nU&e=
> 
> All the best, and thanks for your great work,
> 
>     Mario Emmenlauer
> 
> 
> 
> 
> 
> 
> -- 
> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 M?nchen                          https://urldefense.proofpoint.com/v2/url?u=http-3A__www.marioemmenlauer.de_&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=QqzqULkkGAQzMW7o_z2dpm_jm_J0_enUzW8PBcf33so&e= 
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicrosco
> py.org.uk_mailman_listinfo_ome-2Dusers&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9J
> gXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&
> m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=RXuc9hqsfNP634tZ5Rev-W
> W0RWNmBMarOaHF_vNIBTE&e=

------------------------------

Subject: Digest Footer

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicroscopy.org.uk_mailman_listinfo_ome-2Dusers&d=AwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1zpUuZe4cKPwVedJsQIAUhutw2KjK-dZ7QHotbBNOOA&m=95oqWyM_CRmwmqrdph2osqWbgroqCzv6Tm7jIKB8Kms&s=RXuc9hqsfNP634tZ5Rev-WW0RWNmBMarOaHF_vNIBTE&e= 

------------------------------

End of ome-users Digest, Vol 120, Issue 17
******************************************