From linfordbriant at gmail.com  Mon Aug 13 05:16:18 2018
From: linfordbriant at gmail.com (Linford Briant)
Date: Mon, 13 Aug 2018 10:16:18 +0100
Subject: [Tomviz] tomviz reconstructions publication quality
Message-ID: <CAAKaKL-ULNvnixNokkq=Ec8TfyBg_0_Sa4LuiFv2d=qcEkHsrQ@mail.gmail.com>

Dear Tomviz,

I have used microscopy image browser to segment my objects, and used tomviz
to 3D render my objects (pdf attached).

Now I want to export these images into good quality images that can be
published. However, the exported pngs are low quality.

How would you recommend I make my tomviz reconstructions into a publishable
format? Do I need to go via a different software? If so, which?

Any help on this would be really appreciated!

Kind regards,
Linford
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From marcus.hanwell at kitware.com  Mon Aug 13 16:09:07 2018
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Mon, 13 Aug 2018 16:09:07 -0400
Subject: [Tomviz] tomviz reconstructions publication quality
In-Reply-To: <CAAKaKL-ULNvnixNokkq=Ec8TfyBg_0_Sa4LuiFv2d=qcEkHsrQ@mail.gmail.com>
References: <CAAKaKL-ULNvnixNokkq=Ec8TfyBg_0_Sa4LuiFv2d=qcEkHsrQ@mail.gmail.com>
Message-ID: <CAMkPkZW-JWiV3HYRtnVbEj=e1ENM3B65DypdQ5iqb2ZYozfE+A@mail.gmail.com>

Hi,

On Mon, Aug 13, 2018 at 5:16 AM Linford Briant <linfordbriant at gmail.com>
wrote:

> Dear Tomviz,
>
> I have used microscopy image browser to segment my objects, and used
> tomviz to 3D render my objects (pdf attached).
>

I don't think the PDF made it through, so I can't see what you mention.

>
> Now I want to export these images into good quality images that can be
> published. However, the exported pngs are low quality.
>
> What do you mean here? You can use the palette to change the color palette
(white, black, gray background etc). You can increase the resolution of the
images to be exported. 3D is usually rendered to a raster format, and so to
some extent when publishing you will need to choose a resolution. Tomviz
has been used to produce images used on a few journal covers to date.


> How would you recommend I make my tomviz reconstructions into a
> publishable format? Do I need to go via a different software? If so, which?
>
> You may need to start by being more specific on what you define as "good
quality". We have seen some great visualizations produced with Tomviz that
have been published.

Thanks,

Marcus
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From linfordbriant at gmail.com  Mon Aug 13 16:30:53 2018
From: linfordbriant at gmail.com (Linford Briant)
Date: Mon, 13 Aug 2018 21:30:53 +0100
Subject: [Tomviz] tomviz reconstructions publication quality
In-Reply-To: <CAMkPkZW-JWiV3HYRtnVbEj=e1ENM3B65DypdQ5iqb2ZYozfE+A@mail.gmail.com>
References: <CAAKaKL-ULNvnixNokkq=Ec8TfyBg_0_Sa4LuiFv2d=qcEkHsrQ@mail.gmail.com>
 <CAMkPkZW-JWiV3HYRtnVbEj=e1ENM3B65DypdQ5iqb2ZYozfE+A@mail.gmail.com>
Message-ID: <CAAKaKL-NJMxYFDstkPBuRhy+w5yWpXj8_LWjJKhgm6qZ0cYKLQ@mail.gmail.com>

Hi Marcus,

Thanks for the info below, and sorry about my ignorance. I didn't realise
tomviz was capable of this already!

Basically, as you may have gathered, I'm not familiar with the export
process and formats in tomviz. I have been exporting Figures as .PNG which
is obviously not good (this was the file format I was meant to attached,
not a .pdf). What format would you recommend I export it as if I want to
make a figure in, say, illustrator or coreldraw? Are you exporting images
simply via File > Export Image > etc? Also, how do you change the quality
of the image exported?

Any help on this would be appreciated.

Kind regards,
Linford

On 13 Aug 2018 9:09 p.m., "Marcus D. Hanwell" <marcus.hanwell at kitware.com>
wrote:

Hi,

On Mon, Aug 13, 2018 at 5:16 AM Linford Briant <linfordbriant at gmail.com>
wrote:

> Dear Tomviz,
>
> I have used microscopy image browser to segment my objects, and used
> tomviz to 3D render my objects (pdf attached).
>

I don't think the PDF made it through, so I can't see what you mention.

>
> Now I want to export these images into good quality images that can be
> published. However, the exported pngs are low quality.
>
> What do you mean here? You can use the palette to change the color palette
(white, black, gray background etc). You can increase the resolution of the
images to be exported. 3D is usually rendered to a raster format, and so to
some extent when publishing you will need to choose a resolution. Tomviz
has been used to produce images used on a few journal covers to date.


> How would you recommend I make my tomviz reconstructions into a
> publishable format? Do I need to go via a different software? If so, which?
>
> You may need to start by being more specific on what you define as "good
quality". We have seen some great visualizations produced with Tomviz that
have been published.

Thanks,

Marcus
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From marcus.hanwell at kitware.com  Mon Aug 13 16:38:53 2018
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Mon, 13 Aug 2018 16:38:53 -0400
Subject: [Tomviz] tomviz reconstructions publication quality
In-Reply-To: <CAAKaKL-NJMxYFDstkPBuRhy+w5yWpXj8_LWjJKhgm6qZ0cYKLQ@mail.gmail.com>
References: <CAAKaKL-ULNvnixNokkq=Ec8TfyBg_0_Sa4LuiFv2d=qcEkHsrQ@mail.gmail.com>
 <CAMkPkZW-JWiV3HYRtnVbEj=e1ENM3B65DypdQ5iqb2ZYozfE+A@mail.gmail.com>
 <CAAKaKL-NJMxYFDstkPBuRhy+w5yWpXj8_LWjJKhgm6qZ0cYKLQ@mail.gmail.com>
Message-ID: <CAMkPkZUsPwPTssAWubL6GcAKSwoXY4T99KpxrHfJqtVzQTch3Q@mail.gmail.com>

Hi Linford,

PNG is a good format to export the 3D view, Export Screenshot in 1.4.0
offers a resolution, and a choice of palette. Transparent can be great for
integrating into larger figures, and PNG is an ideal format in my opinion.

I would increase the resolution, but for things like volume rendering,
surfaces, etc it is not easy to export to a vector-based format you might
want to use in Illistrator, but with a high resolution raster rendering
with a transparent background you should be able to make it work.

I hope that helps, you likely want to push above the default resolution
(and we should probably increase that a little).

Thanks,

Marcus

On Mon, Aug 13, 2018 at 4:31 PM Linford Briant <linfordbriant at gmail.com>
wrote:

> Hi Marcus,
>
> Thanks for the info below, and sorry about my ignorance. I didn't realise
> tomviz was capable of this already!
>
> Basically, as you may have gathered, I'm not familiar with the export
> process and formats in tomviz. I have been exporting Figures as .PNG which
> is obviously not good (this was the file format I was meant to attached,
> not a .pdf). What format would you recommend I export it as if I want to
> make a figure in, say, illustrator or coreldraw? Are you exporting images
> simply via File > Export Image > etc? Also, how do you change the quality
> of the image exported?
>
> Any help on this would be appreciated.
>
> Kind regards,
> Linford
>
> On 13 Aug 2018 9:09 p.m., "Marcus D. Hanwell" <marcus.hanwell at kitware.com>
> wrote:
>
> Hi,
>
> On Mon, Aug 13, 2018 at 5:16 AM Linford Briant <linfordbriant at gmail.com>
> wrote:
>
>> Dear Tomviz,
>>
>> I have used microscopy image browser to segment my objects, and used
>> tomviz to 3D render my objects (pdf attached).
>>
>
> I don't think the PDF made it through, so I can't see what you mention.
>
>>
>> Now I want to export these images into good quality images that can be
>> published. However, the exported pngs are low quality.
>>
>> What do you mean here? You can use the palette to change the color
> palette (white, black, gray background etc). You can increase the
> resolution of the images to be exported. 3D is usually rendered to a raster
> format, and so to some extent when publishing you will need to choose a
> resolution. Tomviz has been used to produce images used on a few journal
> covers to date.
>
>
>> How would you recommend I make my tomviz reconstructions into a
>> publishable format? Do I need to go via a different software? If so, which?
>>
>> You may need to start by being more specific on what you define as "good
> quality". We have seen some great visualizations produced with Tomviz that
> have been published.
>
> Thanks,
>
> Marcus
>
>
>
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