What you need to know:
- Demonstrators had been occupying the square in front of the military headquarters since April 6, days before President Omar al-Bashir was overthrown after 30 years in power.
- But on Monday, forces swept in and opened fire on unarmed protesters in the square.
- Protest organisers, the Sudanese Professionals Association (SPA), accused the TMC of carrying out "a massacre" and urged its pro-democracy supporters to continue protesting peacefully.
- In a Facebook post on Wednesday, the Central Committee of Sudanese Doctors said 40 bodies had been recovered from River Nile in the Sudanese capital, Khartoum.
Dozens of bodies have been recovered from the River Nile in the Sudanese capital, Khartoum, following a violent crackdown on pro-democracy protests, opposition activists say.
Doctors linked to the opposition say the 40 bodies are among 100 people believed killed since security forces attacked a protest camp on Monday.
Members of a feared paramilitary group are reported to be attacking civilians.
Sudan's ruling Transitional Military Council (TMC) has vowed to investigate.
Residents in Khartoum have told the BBC they are living in fear as members of the Rapid Support Forces (RSF) roam the streets.
The paramilitary unit - formerly known as the Janjaweed militia - gained notoriety in the Darfur conflict in western Sudan in 2003.
"Forty bodies of our noble martyrs were recovered from the river Nile yesterday," the Central Committee of Sudanese Doctors said in a Facebook post on Wednesday.
An official from the group told the BBC that they had witnessed and verified the bodies in hospitals and that the death toll now stood at 100.
A former security officer quoted by Channel 4's Sudanese journalist Yousra Elbagir said that some of those thrown into the Nile had been beaten or shot to death and others hacked to death with machetes.
"It was a massacre," the unnamed source said.
Demonstrators had been occupying the square in front of the military headquarters since April 6, days before President Omar al-Bashir was overthrown after 30 years in power.
Their representatives had been negotiating with the TMC and agreed a three-year transition that would culminate in elections.
But on Monday, forces swept in and opened fire on unarmed protesters in the square.
On Tuesday, TMC leader General Abdel Fattah al-Burhan announced that negotiations with protesters were over, all previous agreements were cancelled, and elections would be held within nine months.
Demonstrators had demanded a longer period to guarantee fair elections and to dismantle the political network associated with the former government.
International condemnation of the crackdown was swift and on Wednesday Gen Burhan made another televised speech in which he said the TMC was willing to resume negotiations.
"We regret the events," he said, without elaborating.
A TMC spokesman later said an investigation into the deaths of protesters had been launched.
Protesters had called for the Islamic festival of Eid al-Fitr, marked on Tuesday and Wednesday this week, to be celebrated in the streets, as a gesture of defiance against the military.
However, much of Khartoum is under lockdown. Witnesses said protesters had retreated to residential areas where they were building barricades and burning tyres.
Protest organisers, the Sudanese Professionals Association (SPA), accused the TMC of carrying out "a massacre" and urged its pro-democracy supporters to continue protesting peacefully.
"We have reached the point where we can't even step out of our homes because we are scared to be beaten or to be shot by the security forces," one Khartoum resident told the BBC.
Another resident, who also asked not to be named, said he was pulled from his car by members of the Janjaweed and beaten on his head and back.
Large numbers of heavily armed troops were also reported on the streets of Omdurman, Sudan's second-largest city, just across the River Nile from Khartoum.
A woman, identified only as Sulaima, told the BBC that troops from the Rapid Support Forces were "all over Khartoum".
"They're surrounding neighbourhoods, they're threatening people. They're also using live ammunition. They're everywhere. We're not feeling safe and we don't have trust in the security forces. It's complete chaos."
The RSF commander, Mohammed "Hemedti" Hamadan, is a close ally of the United Arab Emirates and Saudi Arabia, Reuters reports, and has sent troops to join the Saudi-led coalition fighting in Yemen's civil war.
December 19, 2018 - Protests erupt after fuel and bread price rises announced
February 22, 2019 - President Bashir dissolves the government
February 24 - Protests continue as security forces respond by firing live bullets
April 6 - Activists begin sit-in at military headquarters, vowing not to move until Mr Bashir steps down
April 11 - Army generals announce that Mr Bashir has been toppled but sit-in continues as people demand civilian rule
April 20 - Talks between the military rulers and civilian representatives begin
May 13 - Shooting outside the military headquarters leaves six people dead
May 14 - Military and civilians announce a deal on a three-year transition period
May 16 - Talks postponed as military demands some barricades are removed
June 3 - Activists announce the suspension of talks with the military, accusing them of using force to disperse their sit-in