histoCAT++ manual

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
milind747
Posts: 2
Joined: Fri Jan 12, 2018 12:19 am

histoCAT++ manual

Post by milind747 » Fri Jan 12, 2018 12:22 am

Hi

I am curious if histocat++ user manual is available for users?

Thanks

Milind

jonas
Site Admin
Posts: 4
Joined: Mon Nov 27, 2017 12:22 pm

Re: histoCAT++ manual

Post by jonas » Fri Jan 12, 2018 10:13 am

Hi Milind

We are currently working on the manual. As soon as it becomes available, we will announce it here.

Jonas

milind747
Posts: 2
Joined: Fri Jan 12, 2018 12:19 am

Re: histoCAT++ manual

Post by milind747 » Fri Jan 12, 2018 9:47 pm

Thank you Jonas.

Milind

sek5317
Posts: 1
Joined: Wed Mar 21, 2018 2:43 pm

Re: histoCAT++ manual

Post by sek5317 » Wed Mar 21, 2018 2:48 pm

To whom it may concern,

I am wondering if there has been any progress on the user manual for Histocat++. I am eager to start using Histocat++, as it seems like a great tool. Please let me know if there is any form of a user manual out there yet. Thanks in advance.

Respectfully,
Sky

RaulCatena
Posts: 25
Joined: Mon Nov 27, 2017 12:49 pm

Re: histoCAT++ manual

Post by RaulCatena » Thu Mar 22, 2018 12:14 pm

Hi Sky

We are a few days away of getting out a first basic manual. Is going to be in web format so it will dynamically grow with additional tutorials for more advanced topics. We will advertise the manual here in the forum as soon as it is available. In the meantime, if you have any urgent question to be able to keep working, feel free to contact me at raul.catena@imls.uzh.ch

Best,

Raúl

RaulCatena
Posts: 25
Joined: Mon Nov 27, 2017 12:49 pm

Re: histoCAT++ manual

Post by RaulCatena » Tue Apr 17, 2018 4:01 pm

Dear histoCAT++ users

We finally have the promised manual ready.
http://www.bodenmillerlab.org/histoCAT_ ... nual_plus/

The format chosen is a typical blog site. This will save us from having different versions circulating. Simply reach out the Bodenmiller laboratory's histoCAT++ site and access the live manual anytime here http://www.bodenmillerlab.com/research-2/histocat-2/

A version of histoCAT++ with improvements is ready to download, so don't forget to upgrade! :)

Regarding the manual, an initial post with general procedures for image visualization is included. Soon we will add more advanced topics.

Feel free to add comments in the blog itself, or post here in the the imc-forum.

We hope this manual is useful for you all.

Regards,

Raúl Catena

MariekeIJsselsteijn
Posts: 4
Joined: Mon Jan 15, 2018 10:52 am

Re: histoCAT++ manual

Post by MariekeIJsselsteijn » Fri Apr 20, 2018 9:32 am

The manual is very clear and concise, thanks for sharing!

I might be wrong but i think the version of Histocat++ that is on the website at the moment is not the newest one. the reason I say this is because it is the same version as i already had and a i am unable to do a few small things that are in the manual. for instance 'rightclicking' the files in the file explorer to load/remove them.

RaulCatena
Posts: 25
Joined: Mon Nov 27, 2017 12:49 pm

Re: histoCAT++ manual

Post by RaulCatena » Fri Apr 20, 2018 10:35 am

Hi Marieke,

I just checked and the version is the last one. Perhaps it could be that the older one "shadows" the newest one if you try opening a workspace by double clicking. I recommend that you erase the old binary (.app file) and move the new download to the Applications folder.

Regards,

ssivajothi
Posts: 30
Joined: Thu Jan 11, 2018 9:00 pm

Re: histoCAT++ manual

Post by ssivajothi » Fri Apr 20, 2018 2:15 pm

Hi Raul,

Thank you for the software and the detailed guide. Looking forward tot he modules on data analysis.

I followed Vito Zanotelli's pipeline for compensation of the .txt file using R. I was able to do this successfully, but Histocat++ says it is not able to load the compensated .txt file. I am able to load the .txt file directly from the Hyperion. Please let me know if you have seen this error and any steps to fix.

Thank you,
Santhosh

RaulCatena
Posts: 25
Joined: Mon Nov 27, 2017 12:49 pm

Re: histoCAT++ manual

Post by RaulCatena » Fri Apr 20, 2018 2:20 pm

Santhosh,

Actually have not tried to load such files yet as histoCAT++ comes with a compensation module already (based on Vito´s paper). Probably is some minor issue on the format of the produced TXT.

Would you mind sharing one of those TXT files so that I can take a quick look? raul.catenafelipe@uzh.ch

Best regards,

Raúl

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