Recently, I finished "Heart of Darkness" by Joseph Conrad... and a theme that is persistent throughout the book is the idea that "The Eyes of Western Civilisation hold back the Heart of Darkness".

I think it's possible to interpret Heart of Darkness that way, but I think it is also possible to read it as very anti Western Imperialism for its dehumanizing practices. The book is somewhat controversial, but I tend towards this interpretation myself.

That said, are Human Rights an invention of western culture... spread over time through territorial acquisition and Colonisation

I think the discourse of Human Rights is actually a post colonial discourse. (Samuel Moyn's The Last Utopia is a good book that makes this point, if you want to read more) So just as a matter of chronology alone I would say that this interpretation can't be right.

And it certainly seems that medieval Europe had a more civilised understanding of "Human Rights" then America or Africa of the same day.

Even if we take a deliberately broad view of the idea of human rights that allows some notion of it to exist in this time period (which I wouldn't do, but for the sake of argument), then this still seems more like 19th century European notions of itself...

I realise that the Europeans did not have the best human rights record upon the initial colonisation of certain regions... but even then, the natives seemed to be protected from Tribal wars and racial genocide that occurred without the European masters

This is the classic idea of the "civilizing mission" of 19th century Imperialism. Many European rulers seemed to genuinely believe it, or at least used it to justify their otherwise economically or politically motivated actions. To be frank though, by today's standards it is Eurocentric and frankly bordering on offensive.

but even then, the natives seemed to be protected from Tribal wars and racial genocide that occurred without the European masters. And it certainly seems that medieval Europe had a more civilised understanding of "Human Rights" then America or Africa of the same day.

Wars and racial genocide were commonly inflicted on native people by colonial powers. When it comes down to it, people making this argument are often walking into the trap of arguing that it's better to be wiped out completely than to have constant low-level warfare.

You can see this in southern Africa. Early Dutch settlers in the Cape in the 18^th century and the German colonialists in Namibia in the late 19^th and early 20^th centuries both embarked on genocidal campaigns against the native San people. Dutch settlers would run commandos against San groups, killing the men but often keeping women and children as slaves. Later German rulers in Namibia purposefully set up a series of restrictive laws allowing San to be shot for many reasons such as fleeing from police, knowing full well that this meant that police would almost always have a reason to kill San. That's not even including unofficial hunting of San people, or German farmers who captured San women as sex slaves.

In 1904 the Herero and Nama in Namibia rose against German rule for a number of reasons including land dispossession, loss of political power, and abuses by German authorities. The Germans responded by killing tens of thousands of Herero, the vast majority, and thousands of Nama, around a third of their population, as well as nearly wiping out the main Nama clans involved in resistance.

This is, indeed, not the best human rights record. My point here is that natives were not better off under colonialism. It's true that there was frequent warfare within the Nama and between the Nama and Herero, and that the San occasionally came into violent conflict with both groups. However, all these groups often did get along. They also never attempted to completely destroy each other, so "racial genocide" was not an issue they faced before the rule of the Germans. In fact, they often joined together against their new enemies; many San captains joined with the Herero or Nama in resistance, and one of the great resistance leaders, Jacob Morenga, was half Herero and half Nama.

No matter how much infrastructure, medicine, "civilization", &c, the Germans brought to Namibia, it still came at the cost of subjugating native peoples and destroying entire nations, and the Germans, like many other colonial powers, never intended for the natives to benefit from any of these anyways (see: Manifest Destiny, Congo Free State, Australia).

It's become fashionable- and in fact, despite what some "edgy" public intellectuals will tell you, nearly always has been, except for a few academic and activist subcultures- to argue that no, really, colonialism was pretty okay. It's not.

Sources:

Marion Wallace, A History of Namibia

Nigel Penn, The Forgotten Frontier: Colonist and Khoisan on the Cape's Northern Frontier in the 18^th Century

Robert Gordon and Stuart Sholto-Douglas, The Bushman Myth: the Making of a Namibian Underclass

Report on the Natives of South-West Africa and their treatment by Germany (this was published in 1918; it was a report by the Union of South Africa after it acquired Namibia in WWI. As such, it has very outdated views of native cultures and is also clearly anti-German propaganda. However, it's useful, and it's easily available on the internet)

EDIT: formatting

The topic of human rights is an interesting question. I am suspicious of your evaluations of colonizers and colonized peoples, but the topic of human rights is certainly interesting. Here are a couple of questions to keep in mind:

(1) Do you mean legal human rights, or moral human rights? If you're thinking of moral human rights then you're going to have to go back much farther in time to find an answer than you would with legal human rights which are very definitely a product of the second half of the 20th century. You'd also have to figure out just where you want to draw the line when it comes to defining a moral human right Would you count pronouncements and obligations regarding the innate dignity of humanity found in religious texts as being evidence of a culture of human rights? If so, it seems that every culture has some rudimentary notion of human rights. But you want to be more specific then that. Well what then about medieval European society leads you to think that it had culture of moral human rights? It certainly did not have one of legal human rights. Why do you say that medieval Europe had human rights, whereas other cultures did not?

(2) What do you mean by an "invention"? If the question is: "Are modern legal human rights primarily a product of Western states exercising their influence/prerogatives in the international realm against the objections/neutrality/apathy of other states?" I think the answer is "no." As Allen Buchanan (among many others) has pointed out, the drafting of the UN Declaration of Human Rights was heavily influenced by the input of formerly colonized third world nations who, as a group, were largely supportive of the document, even more so than powerful nations like the U.S. and Great Britain.

Source: The Heart of Human Rights - Allen Buchanan