# Big TIFF problem

**URL:** <https://discourse.itk.org/t/big-tiff-problem/831>\
**Category:** Engineering\
**Created:** [April 8, 2018, 11:16pm UTC](https://discourse.itk.org/t/big-tiff-problem/831 "2018-04-08T23:16:20Z")\
**Posts on this page:** 13\
**Page:** 2

<div class="post-metadata">

**Author:** ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Post date:** [April 10, 2018, 10:20am UTC](https://discourse.itk.org/t/big-tiff-problem/831/22 "2018-04-10T10:20:48Z")

</div>

Do you have git installed? Are you behind a proxy? What is your OS?

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 10:24am UTC](https://discourse.itk.org/t/big-tiff-problem/831/23 "2018-04-10T10:24:47Z")

</div>

I do have git installed, and use it to store software on github. I am using Windows 7, and no proxy as far as I know.

---

<div class="post-metadata">

**Author:** ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Post date:** [April 10, 2018, 10:31am UTC](https://discourse.itk.org/t/big-tiff-problem/831/24 "2018-04-10T10:31:16Z")

</div>

> [@Gib](#):
>
> [GitHub - scifio/scifio-imageio: SCIFIO ImageIO plugin for ITK](https://github.com/scifio/scifio-imageio.git)

Can you try:

```auto
git clone https://github.com/scifio/scifio-imageio.git delete_me_scifio

```

just to check if it is a cmake problem or git…

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 10:31am UTC](https://discourse.itk.org/t/big-tiff-problem/831/25 "2018-04-10T10:31:34Z")

</div>

When I try the clone from the command line I get this:  
D:\>git clone [https://github.com/scifio/scifio-imageio.git](https://github.com/scifio/scifio-imageio.git)  
Cloning into ‘scifio-imageio’…  
fatal: unable to access ‘[https://github.com/scifio/scifio-imageio.git/](https://github.com/scifio/scifio-imageio.git/)’: error:1  
407742E:SSL routines:SSL23\_GET\_SERVER\_HELLO:tlsv1 alert protocol version

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 10:33am UTC](https://discourse.itk.org/t/big-tiff-problem/831/26 "2018-04-10T10:33:52Z")

</div>

With delete\_me\_scifio I get the same error.

---

<div class="post-metadata">

**Author:** ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Post date:** [April 10, 2018, 10:34am UTC](https://discourse.itk.org/t/big-tiff-problem/831/27 "2018-04-10T10:34:28Z")

</div>

Umm reading from [here](https://github.com/desktop/desktop/issues/3165). It seems that might be worthy try to reinstall git for windows, get the latest version.

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 10:36am UTC](https://discourse.itk.org/t/big-tiff-problem/831/28 "2018-04-10T10:36:36Z")

</div>

I’ll do that.

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 11:09am UTC](https://discourse.itk.org/t/big-tiff-problem/831/29 "2018-04-10T11:09:49Z")

</div>

That fixed it. I’m now rebuilding ITK.

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 11:43am UTC](https://discourse.itk.org/t/big-tiff-problem/831/30 "2018-04-10T11:43:30Z")

</div>

I was able to add the SCIFIO code to my program and build it.  
But running it gives an odd result. An error popup “Java Virtual Machine Launcher” appears with:  
Could not find the main class: loci.scifio.itk.SCIFIOITKBridge. Program will exit.

By the way without the SCIFIO code the program behaved just as before, finding only one slice.

---

<div class="post-metadata">

**Author:** ![phcerdan](https://discourse.itk.org/user_avatar/discourse.itk.org/phcerdan/32/286_2.png) [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Post date:** [April 10, 2018, 11:53am UTC](https://discourse.itk.org/t/big-tiff-problem/831/31 "2018-04-10T11:53:59Z")

</div>

That seems like a java problem. Do you have it installed system wide?  
Can you type `java -version` in the console?

Or maybe `JAVA_HOME` is unset.

---

<div class="post-metadata">

**Author:** ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Post date:** [April 10, 2018, 1:55pm UTC](https://discourse.itk.org/t/big-tiff-problem/831/32 "2018-04-10T13:55:29Z")

</div>

@Gib There have been many fixes to the SCIFIO module in recent ITK. It is best to try ITK 4.13 or ITK 5.

---

<div class="post-metadata">

**Author:** ![Gib](https://discourse.itk.org/user_avatar/discourse.itk.org/gib/32/4124_2.png) [@Gib](https://discourse.itk.org/u/Gib)\
**Post date:** [April 10, 2018, 7:44pm UTC](https://discourse.itk.org/t/big-tiff-problem/831/33 "2018-04-10T19:44:09Z")

</div>

I can see java system-wide:  
java version “1.8.0\_151”  
Java™ SE Runtime Environment (build 1.8.0\_151-b12)  
Java HotSpot™ 64-Bit Server VM (build 25.151-b12, mixed mode)

but java\_home is not set. I will explore setting that,

But the problem may be solved at the other end. The person who creates these tiffs with ImageJ has just informed me that he has found a way to export them with BioFormats that generates big tiffs readable by my program.

Thanks for all the help, Pablo.

---

<div class="post-metadata">

**Author:** ![ctrueden](https://discourse.itk.org/user_avatar/discourse.itk.org/ctrueden/32/38_2.png) [@ctrueden](https://discourse.itk.org/u/ctrueden)\
**Post date:** [June 21, 2018, 2:05pm UTC](https://discourse.itk.org/t/big-tiff-problem/831/34 "2018-06-21T14:05:44Z")

</div>

> [@Gib](#):
>
> Do you know of a Windows program that I could use for this?

@Gib Sorry for the late reply. You can install [Cygwin](http://cygwin.com/), which enables usage of many \*nix-based tools on Windows. I recommend using [Chocolatey](https://chocolatey.org/) to install packages on Windows. Alternately, you could try the [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10) on a Windows 10 system.

[Previous page](https://discourse.itk.org/t/big-tiff-problem/831.md?page=1)